Variant rs104886478 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 1P and 3B. PP5BP4BP7BS2_Supporting

The NM_001142459.2(ASB10):c.810C>T(p.Thr270=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000207 in 1,613,074 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 Pathogenic (no stars).

Frequency

Genomes: 𝑓 0.00032 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00020 ( 1 hom. )

Consequence

ASB10
NM_001142459.2 synonymous

Scores

Clinical Significance

Pathogenic no assertion criteria provided P:1O:1

Conservation

PhyloP100: -1.84

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 Likely_benign. Variant got -2 ACMG points.

PP5

Variant 7-151181233-G-A is Pathogenic according to our data. Variant chr7-151181233-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 50951.Status of the report is no_assertion_criteria_provided, 0 stars.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87). . Strength limited to SUPPORTING due to the PP5.

BP7

Synonymous conserved (PhyloP=-1.84 with no splicing effect.

BS2

High AC in GnomAd4 at 48 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ASB10	NM_001142459.2 linkuse as main transcript	c.810C>T	p.Thr270=	synonymous_variant	3/6	ENST00000420175.3
ASB10	NM_080871.4 linkuse as main transcript	c.765C>T	p.Thr255=	synonymous_variant	3/6
ASB10	NM_001142460.1 linkuse as main transcript	c.810C>T	p.Thr270=	synonymous_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASB10	ENST00000420175.3 linkuse as main transcript	c.810C>T	p.Thr270=	synonymous_variant	3/6	1	NM_001142459.2	P4	Q8WXI3-1
ASB10	ENST00000275838.5 linkuse as main transcript	c.810C>T	p.Thr270=	synonymous_variant	3/5	1			Q8WXI3-2
ASB10	ENST00000377867.7 linkuse as main transcript	c.765C>T	p.Thr255=	synonymous_variant	3/6	2		A1	Q8WXI3-3

Frequencies

GnomAD3 genomes

AF:

0.000315

AC:

AN:

152244

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00395

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000500

AC:

124

AN:

248062

Hom.:

AF XY:

0.000475

AC XY:

AN XY:

134846

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000523

Gnomad FIN exome

AF:

0.00429

Gnomad NFE exome

AF:

0.000117

Gnomad OTH exome

AF:

0.000494

GnomAD4 exome

AF:

0.000196

AC:

286

AN:

1460712

Hom.:

Cov.:

AF XY:

0.000201

AC XY:

146

AN XY:

726696

show subpopulations

Gnomad4 AFR exome

AF:

0.0000299

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000348

Gnomad4 FIN exome

AF:

0.00378

Gnomad4 NFE exome

AF:

0.0000378

Gnomad4 OTH exome

AF:

0.000232

GnomAD4 genome

AF:

0.000315

AC:

AN:

152362

Hom.:

Cov.:

AF XY:

0.000470

AC XY:

AN XY:

74510

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000621

Gnomad4 FIN

AF:

0.00395

Gnomad4 NFE

AF:

0.0000147

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000136

Hom.:

Bravo

AF:

0.0000340

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.0000545

EpiControl

AF:

0.00

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Glaucoma 1, open angle, F

Pathogenic:1Other:1

not provided, no classification provided	literature only	Casey Eye Institute Glaucoma Genetics Lab	-	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Mar 15, 2012	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.15

DANN

Benign

0.62

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