Variant 9-129638381-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The ENST00000277458.5(ASB6):c.675G>A(p.Val225Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00519 in 1,613,724 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0032 ( 2 hom., cov: 33)

Exomes 𝑓: 0.0054 ( 24 hom. )

Consequence

ASB6
ENST00000277458.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.995

Variant links:

Genes affected

ASB6 (HGNC:17181): (ankyrin repeat and SOCS box containing 6) The protein encoded by this gene belongs to a family of ankyrin repeat proteins that, along with four other protein families, contain a C-terminal SOCS box motif. Growing evidence suggests that the SOCS box, similar to the F-box, acts as a bridge between specific substrate-binding domains and the more generic proteins that comprise a large family of E3 ubiquitin protein ligases. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Jan 2011]

ASB6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_addAF=-0.48557).

BP6

Variant 9-129638381-C-T is Benign according to our data. Variant chr9-129638381-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2659573.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.995 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASB6	NM_017873.4 linkuse as main transcript	c.675G>A	p.Val225Val	synonymous_variant	6/6	ENST00000277458.5	NP_060343.1	Q9NWX5-1
ASB6	NM_177999.3 linkuse as main transcript	c.566G>A	p.Trp189*	stop_gained	5/5		NP_821066.1	Q9NWX5-2
ASB6	NM_001202403.2 linkuse as main transcript	c.588G>A	p.Val196Val	synonymous_variant	5/5		NP_001189332.1	Q9NWX5F6TX30

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ASB6	ENST00000277459.8 linkuse as main transcript	c.566G>A	p.Trp189*	stop_gained	5/5	1		ENSP00000277459.4	Q9NWX5-2
ASB6	ENST00000277458.5 linkuse as main transcript	c.675G>A	p.Val225Val	synonymous_variant	6/6	1	NM_017873.4	ENSP00000277458.4	Q9NWX5-1
ASB6	ENST00000450050.6 linkuse as main transcript	c.588G>A	p.Val196Val	synonymous_variant	5/5	1		ENSP00000416172.3	F6TX30

Frequencies

GnomAD3 genomes

AF:

0.00321

AC:

489

AN:

152164

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00118

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.00170

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00576

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00297

AC:

743

AN:

249824

Hom.:

AF XY:

0.00314

AC XY:

424

AN XY:

135212

show subpopulations

Gnomad AFR exome

AF:

0.000989

Gnomad AMR exome

AF:

0.00147

Gnomad ASJ exome

AF:

0.000199

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00121

Gnomad FIN exome

AF:

0.000234

Gnomad NFE exome

AF:

0.00542

Gnomad OTH exome

AF:

0.00359

GnomAD4 exome

AF:

0.00539

AC:

7884

AN:

1461442

Hom.:

Cov.:

AF XY:

0.00519

AC XY:

3772

AN XY:

727020

show subpopulations

Gnomad4 AFR exome

AF:

0.000478

Gnomad4 AMR exome

AF:

0.00172

Gnomad4 ASJ exome

AF:

0.000306

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00162

Gnomad4 FIN exome

AF:

0.000509

Gnomad4 NFE exome

AF:

0.00657

Gnomad4 OTH exome

AF:

0.00503

GnomAD4 genome

AF:

0.00322

AC:

490

AN:

152282

Hom.:

Cov.:

AF XY:

0.00293

AC XY:

218

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.00118

Gnomad4 AMR

AF:

0.00170

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.000188

Gnomad4 NFE

AF:

0.00578

Gnomad4 OTH

AF:

0.00378

Alfa

AF:

0.00516

Hom.:

Bravo

AF:

0.00320

TwinsUK

AF:

0.00674

AC:

ALSPAC

AF:

0.00571

AC:

ESP6500AA

AF:

0.00136

AC:

ESP6500EA

AF:

0.00698

AC:

ExAC

AF:

0.00312

AC:

379

EpiCase

AF:

0.00556

EpiControl

AF:

0.00504

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

ASB6: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.49

BayesDel_noAF

Benign

-0.46

CADD

Benign

7.9

DANN

Uncertain

0.99

Eigen

Benign

-0.13

Eigen_PC

Benign

-0.080

FATHMM_MKL

Uncertain

0.88

MutationTaster

Benign

1.0

D;D;N

Vest4

0.12

GERP RS

3.5

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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