Variant chr20-1578429-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6BP7

The NM_006065.5(SIRPB1):c.342C>T(p.Asp114=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000164 in 145,938 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00016 ( 1 hom., cov: 29)

Exomes 𝑓: 0.0023 ( 516 hom. )

Failed GnomAD Quality Control

Consequence

SIRPB1
NM_006065.5 synonymous

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.00600

Variant links:

Genes affected

SIRPB1 (HGNC:15928): (signal regulatory protein beta 1) The protein encoded by this gene is a member of the signal-regulatory-protein (SIRP) family, and also belongs to the immunoglobulin superfamily. SIRP family members are receptor-type transmembrane glycoproteins known to be involved in the negative regulation of receptor tyrosine kinase-coupled signaling processes. This protein was found to interact with TYROBP/DAP12, a protein bearing immunoreceptor tyrosine-based activation motifs. This protein was also reported to participate in the recruitment of tyrosine kinase SYK. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009]

SIRPB1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 20-1578429-G-A is Benign according to our data. Variant chr20-1578429-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2681546.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.006 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
SIRPB1	NM_006065.5 linkuse as main transcript	c.342C>T	p.Asp114=	synonymous_variant	2/6	ENST00000381605.9
SIRPB1	NM_001083910.4 linkuse as main transcript	c.342C>T	p.Asp114=	synonymous_variant	2/4
SIRPB1	NM_001330639.2 linkuse as main transcript	c.339C>T	p.Asp113=	synonymous_variant	2/4
SIRPB1	XM_005260641.4 linkuse as main transcript	c.339C>T	p.Asp113=	synonymous_variant	2/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SIRPB1	ENST00000381605.9 linkuse as main transcript	c.342C>T	p.Asp114=	synonymous_variant	2/6	1	NM_006065.5		O00241-1

Frequencies

GnomAD3 genomes

AF:

0.000165

AC:

AN:

145824

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000397

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000273

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000459

Gnomad OTH

AF:

0.000509

GnomAD3 exomes

AF:

0.000190

AC:

AN:

247668

Hom.:

AF XY:

0.000224

AC XY:

AN XY:

133888

show subpopulations

Gnomad AFR exome

AF:

0.000680

Gnomad AMR exome

AF:

0.0000581

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000984

Gnomad FIN exome

AF:

0.000243

Gnomad NFE exome

AF:

0.000224

Gnomad OTH exome

AF:

0.000166

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00227

AC:

3088

AN:

1362180

Hom.:

516

Cov.:

AF XY:

0.00221

AC XY:

1502

AN XY:

680278

show subpopulations

Gnomad4 AFR exome

AF:

0.00149

Gnomad4 AMR exome

AF:

0.000317

Gnomad4 ASJ exome

AF:

0.000395

Gnomad4 EAS exome

AF:

0.000204

Gnomad4 SAS exome

AF:

0.000499

Gnomad4 FIN exome

AF:

0.00262

Gnomad4 NFE exome

AF:

0.00268

Gnomad4 OTH exome

AF:

0.00151

GnomAD4 genome

AF:

0.000164

AC:

AN:

145938

Hom.:

Cov.:

AF XY:

0.000198

AC XY:

AN XY:

70820

show subpopulations

Gnomad4 AFR

AF:

0.000396

Gnomad4 AMR

AF:

0.000272

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000459

Gnomad4 OTH

AF:

0.000504

Alfa

AF:

0.000461

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

EBV-positive nodal T- and NK-cell lymphoma

Benign:1

Likely benign, no assertion criteria provided

research

Department of Clinical Pathology, School of Medicine, Fujita Health University

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

DANN

Benign

0.73

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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