NM_001384900.1(SEMA3D):c.1272C>A (p.His424Gln) AND not provided

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Mar 1, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000950415.15

Allele description [Variation Report for NM_001384900.1(SEMA3D):c.1272C>A (p.His424Gln)]

NM_001384900.1(SEMA3D):c.1272C>A (p.His424Gln)

Gene:

SEMA3D:semaphorin 3D [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q21.11

Genomic location:

Preferred name:

NM_001384900.1(SEMA3D):c.1272C>A (p.His424Gln)

HGVS:

NC_000007.14:g.85022533G>T
NG_051329.1:g.169323C>A
NM_001384900.1:c.1272C>AMANE SELECT
NM_001384901.1:c.1272C>A
NM_001384902.1:c.1272C>A
NM_001384903.1:c.1272C>A
NM_152754.3:c.1272C>A
NP_001371829.1:p.His424Gln
NP_001371830.1:p.His424Gln
NP_001371831.1:p.His424Gln
NP_001371832.1:p.His424Gln
NP_689967.2:p.His424Gln
NP_689967.2:p.His424Gln
NC_000007.13:g.84651849G>T
NM_152754.2:c.1272C>A
p.(His424Gln)

Protein change:

H424Q

Links:

dbSNP: rs141893504

NCBI 1000 Genomes Browser:

rs141893504

Molecular consequence:

NM_001384900.1:c.1272C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384901.1:c.1272C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384902.1:c.1272C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384903.1:c.1272C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_152754.3:c.1272C>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV001096721	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Dec 31, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004162418	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Mar 1, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001096721

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Dec 31, 2019)

germline

clinical testing

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

SCV004162418

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Benign
(Mar 1, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	4	not provided	not provided	not provided	not provided	clinical testing
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, SCV001096721.2

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

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV004162418.10

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	not provided	not provided	clinical testing	not provided

Description

SEMA3D: BS1, BS2

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		4	not provided	not provided	not provided

Last Updated: Nov 3, 2024

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