Variant 3-122911476-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001031702.4(SEMA5B):c.3091+15A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 1,601,644 control chromosomes in the GnomAD database, including 503,724 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.71 ( 40081 hom., cov: 33)

Exomes 𝑓: 0.79 ( 463643 hom. )

Consequence

SEMA5B
NM_001031702.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0330

Variant links:

Genes affected

SEMA5B (HGNC:10737): (semaphorin 5B) This gene encodes a member of the semaphorin protein family which regulates axon growth during development of the nervous system. The encoded protein has a characteristic Sema domain near the N-terminus, through which semaphorins bind to plexin, and five thrombospondin type 1 repeats in the C-terminal region of the protein. The protein product may be cleaved and exist as a secreted molecule (PMID: 19463192). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

SEMA5B links:

SEMA5B (HGNC:):

SEMA5B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 3-122911476-T-G is Benign according to our data. Variant chr3-122911476-T-G is described in ClinVar as [Benign]. Clinvar id is 1224885.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEMA5B	NM_001031702.4 linkuse as main transcript	c.3091+15A>C		intron_variant		ENST00000357599.8	NP_001026872.2	Q9P283-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEMA5B	ENST00000357599.8 linkuse as main transcript	c.3091+15A>C		intron_variant		1	NM_001031702.4	ENSP00000350215.3		Q9P283-1

Frequencies

GnomAD3 genomes

AF:

0.715

AC:

108405

AN:

151666

Hom.:

40068

Cov.:

show subpopulations

Gnomad AFR

AF:

0.585

Gnomad AMI

AF:

0.863

Gnomad AMR

AF:

0.636

Gnomad ASJ

AF:

0.776

Gnomad EAS

AF:

0.335

Gnomad SAS

AF:

0.714

Gnomad FIN

AF:

0.733

Gnomad MID

AF:

0.835

Gnomad NFE

AF:

0.831

Gnomad OTH

AF:

0.742

GnomAD3 exomes

AF:

0.706

AC:

162081

AN:

229678

Hom.:

60019

AF XY:

0.720

AC XY:

88697

AN XY:

123274

show subpopulations

Gnomad AFR exome

AF:

0.575

Gnomad AMR exome

AF:

0.513

Gnomad ASJ exome

AF:

0.780

Gnomad EAS exome

AF:

0.328

Gnomad SAS exome

AF:

0.729

Gnomad FIN exome

AF:

0.727

Gnomad NFE exome

AF:

0.827

Gnomad OTH exome

AF:

0.748

GnomAD4 exome

AF:

0.792

AC:

1147875

AN:

1449860

Hom.:

463643

Cov.:

AF XY:

0.791

AC XY:

569593

AN XY:

719724

show subpopulations

Gnomad4 AFR exome

AF:

0.575

Gnomad4 AMR exome

AF:

0.526

Gnomad4 ASJ exome

AF:

0.788

Gnomad4 EAS exome

AF:

0.304

Gnomad4 SAS exome

AF:

0.734

Gnomad4 FIN exome

AF:

0.736

Gnomad4 NFE exome

AF:

0.834

Gnomad4 OTH exome

AF:

0.767

GnomAD4 genome

AF:

0.715

AC:

108458

AN:

151784

Hom.:

40081

Cov.:

AF XY:

0.708

AC XY:

52518

AN XY:

74142

show subpopulations

Gnomad4 AFR

AF:

0.584

Gnomad4 AMR

AF:

0.635

Gnomad4 ASJ

AF:

0.776

Gnomad4 EAS

AF:

0.335

Gnomad4 SAS

AF:

0.715

Gnomad4 FIN

AF:

0.733

Gnomad4 NFE

AF:

0.831

Gnomad4 OTH

AF:

0.743

Alfa

AF:

0.804

Hom.:

84172

Bravo

AF:

0.696

Asia WGS

AF:

0.588

AC:

2048

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.3

DANN

Benign

0.13

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over