NM_022367.4(SEMA4A):c.196A>C (p.Thr66Pro) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 19, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001309424.7

Allele description [Variation Report for NM_022367.4(SEMA4A):c.196A>C (p.Thr66Pro)]

NM_022367.4(SEMA4A):c.196A>C (p.Thr66Pro)

Gene:

SEMA4A:semaphorin 4A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q22

Genomic location:

Preferred name:

NM_022367.4(SEMA4A):c.196A>C (p.Thr66Pro)

HGVS:

NC_000001.11:g.156156470A>C
NG_027683.1:g.11527A>C
NM_001193300.2:c.196A>C
NM_001193301.2:c.196A>C
NM_001193302.2:c.-102A>C
NM_001370567.1:c.196A>C
NM_001370568.1:c.-102A>C
NM_001370569.1:c.-329A>C
NM_001370571.1:c.-329A>C
NM_022367.3:c.196A>C
NM_022367.4:c.196A>CMANE SELECT
NP_001180229.1:p.Thr66Pro
NP_001180230.1:p.Thr66Pro
NP_001357496.1:p.Thr66Pro
NP_071762.2:p.Thr66Pro
NC_000001.10:g.156126261A>C

Protein change:

T66P

Links:

dbSNP: rs773118228

NCBI 1000 Genomes Browser:

rs773118228

Molecular consequence:

NM_001193302.2:c.-102A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370568.1:c.-102A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370569.1:c.-329A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370571.1:c.-329A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001193300.2:c.196A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001193301.2:c.196A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370567.1:c.196A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_022367.4:c.196A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001498921	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 19, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001498921

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 19, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001498921.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant has not been reported in the literature in individuals affected with SEMA4A-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 1011600). This variant is present in population databases (rs773118228, gnomAD 0.004%). This sequence change replaces threonine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 66 of the SEMA4A protein (p.Thr66Pro).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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