Variant chr7-151181173-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001142459.2(ASB10):c.870G>C(p.Ala290=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 1,610,130 control chromosomes in the GnomAD database, including 127,099 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.47 ( 19071 hom., cov: 33)

Exomes 𝑓: 0.38 ( 108028 hom. )

Consequence

ASB10
NM_001142459.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -3.65

Variant links:

Genes affected

ASB10 (HGNC:17185): (ankyrin repeat and SOCS box containing 10) The protein encoded by this gene is a member of the ankyrin repeat and SOCS box-containing (ASB) family of proteins. The SOCS box serves to couple suppressor of cytokine signaling (SOCS) proteins and their binding partners with the elongin B and C complex, possibly targeting them for degradation. Multiple alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Dec 2008]

ASB10 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 7-151181173-C-G is Benign according to our data. Variant chr7-151181173-C-G is described in ClinVar as [Benign]. Clinvar id is 667623.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.65 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ASB10	NM_001142459.2 linkuse as main transcript	c.870G>C	p.Ala290=	synonymous_variant	3/6	ENST00000420175.3	NP_001135931.2
ASB10	NM_080871.4 linkuse as main transcript	c.825G>C	p.Ala275=	synonymous_variant	3/6		NP_543147.2
ASB10	NM_001142460.1 linkuse as main transcript	c.870G>C	p.Ala290=	synonymous_variant	3/5		NP_001135932.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASB10	ENST00000420175.3 linkuse as main transcript	c.870G>C	p.Ala290=	synonymous_variant	3/6	1	NM_001142459.2	ENSP00000391137	P4	Q8WXI3-1
ASB10	ENST00000275838.5 linkuse as main transcript	c.870G>C	p.Ala290=	synonymous_variant	3/5	1		ENSP00000275838		Q8WXI3-2
ASB10	ENST00000377867.7 linkuse as main transcript	c.825G>C	p.Ala275=	synonymous_variant	3/6	2		ENSP00000367098	A1	Q8WXI3-3

Frequencies

GnomAD3 genomes

AF:

0.475

AC:

72180

AN:

152096

Hom.:

19038

Cov.:

show subpopulations

Gnomad AFR

AF:

0.722

Gnomad AMI

AF:

0.299

Gnomad AMR

AF:

0.387

Gnomad ASJ

AF:

0.464

Gnomad EAS

AF:

0.536

Gnomad SAS

AF:

0.301

Gnomad FIN

AF:

0.379

Gnomad MID

AF:

0.363

Gnomad NFE

AF:

0.369

Gnomad OTH

AF:

0.472

GnomAD3 exomes

AF:

0.399

AC:

97166

AN:

243776

Hom.:

20757

AF XY:

0.389

AC XY:

51702

AN XY:

132890

show subpopulations

Gnomad AFR exome

AF:

0.731

Gnomad AMR exome

AF:

0.338

Gnomad ASJ exome

AF:

0.464

Gnomad EAS exome

AF:

0.531

Gnomad SAS exome

AF:

0.291

Gnomad FIN exome

AF:

0.389

Gnomad NFE exome

AF:

0.374

Gnomad OTH exome

AF:

0.389

GnomAD4 exome

AF:

0.378

AC:

551455

AN:

1457916

Hom.:

108028

Cov.:

AF XY:

0.375

AC XY:

271961

AN XY:

724924

show subpopulations

Gnomad4 AFR exome

AF:

0.730

Gnomad4 AMR exome

AF:

0.347

Gnomad4 ASJ exome

AF:

0.467

Gnomad4 EAS exome

AF:

0.540

Gnomad4 SAS exome

AF:

0.294

Gnomad4 FIN exome

AF:

0.387

Gnomad4 NFE exome

AF:

0.366

Gnomad4 OTH exome

AF:

0.404

GnomAD4 genome

AF:

0.475

AC:

72262

AN:

152214

Hom.:

19071

Cov.:

AF XY:

0.468

AC XY:

34855

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.722

Gnomad4 AMR

AF:

0.386

Gnomad4 ASJ

AF:

0.464

Gnomad4 EAS

AF:

0.536

Gnomad4 SAS

AF:

0.303

Gnomad4 FIN

AF:

0.379

Gnomad4 NFE

AF:

0.369

Gnomad4 OTH

AF:

0.471

Alfa

AF:

0.359

Hom.:

3026

Bravo

AF:

0.491

Asia WGS

AF:

0.420

AC:

1462

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 02, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.0040

DANN

Benign

0.43

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