Variant chr7-151181019-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_001142459.2(ASB10):c.1024C>T(p.Leu342=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00524 in 1,606,700 control chromosomes in the GnomAD database, including 68 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0040 ( 6 hom., cov: 33)

Exomes 𝑓: 0.0054 ( 62 hom. )

Consequence

ASB10
NM_001142459.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2O:1

Conservation

PhyloP100: 0.341

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 -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 7-151181019-G-A is Benign according to our data. Variant chr7-151181019-G-A is described in ClinVar as [Benign]. Clinvar id is 99990.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.341 with no splicing effect.

BS2

High AC in GnomAd4 at 603 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ASB10	NM_001142459.2 linkuse as main transcript	c.1024C>T	p.Leu342=	synonymous_variant	3/6	ENST00000420175.3	NP_001135931.2
ASB10	NM_080871.4 linkuse as main transcript	c.979C>T	p.Leu327=	synonymous_variant	3/6		NP_543147.2
ASB10	NM_001142460.1 linkuse as main transcript	c.1024C>T	p.Leu342=	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.1024C>T	p.Leu342=	synonymous_variant	3/6	1	NM_001142459.2	ENSP00000391137	P4	Q8WXI3-1
ASB10	ENST00000275838.5 linkuse as main transcript	c.1024C>T	p.Leu342=	synonymous_variant	3/5	1		ENSP00000275838		Q8WXI3-2
ASB10	ENST00000377867.7 linkuse as main transcript	c.979C>T	p.Leu327=	synonymous_variant	3/6	2		ENSP00000367098	A1	Q8WXI3-3

Frequencies

GnomAD3 genomes

AF:

0.00397

AC:

604

AN:

152244

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00116

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00320

Gnomad ASJ

AF:

0.0467

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.000470

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00451

Gnomad OTH

AF:

0.0115

GnomAD3 exomes

AF:

0.00510

AC:

1240

AN:

243130

Hom.:

AF XY:

0.00525

AC XY:

698

AN XY:

132902

show subpopulations

Gnomad AFR exome

AF:

0.000580

Gnomad AMR exome

AF:

0.00302

Gnomad ASJ exome

AF:

0.0460

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00239

Gnomad FIN exome

AF:

0.000529

Gnomad NFE exome

AF:

0.00507

Gnomad OTH exome

AF:

0.00716

GnomAD4 exome

AF:

0.00538

AC:

7818

AN:

1454338

Hom.:

Cov.:

AF XY:

0.00538

AC XY:

3889

AN XY:

722258

show subpopulations

Gnomad4 AFR exome

AF:

0.00123

Gnomad4 AMR exome

AF:

0.00346

Gnomad4 ASJ exome

AF:

0.0484

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00244

Gnomad4 FIN exome

AF:

0.000698

Gnomad4 NFE exome

AF:

0.00503

Gnomad4 OTH exome

AF:

0.00748

GnomAD4 genome

AF:

0.00396

AC:

603

AN:

152362

Hom.:

Cov.:

AF XY:

0.00382

AC XY:

285

AN XY:

74516

show subpopulations

Gnomad4 AFR

AF:

0.00115

Gnomad4 AMR

AF:

0.00320

Gnomad4 ASJ

AF:

0.0467

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.000470

Gnomad4 NFE

AF:

0.00451

Gnomad4 OTH

AF:

0.0114

Alfa

AF:

0.00769

Hom.:

Bravo

AF:

0.00467

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.00611

EpiControl

AF:

0.00557

ClinVar

Significance: Benign

Submissions summary: Benign:2Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Nov 06, 2023	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Glaucoma 1, open angle, F

Other:1

not provided, no classification provided

literature only

Casey Eye Institute Glaucoma Genetics Lab

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

5.2

DANN

Benign

0.68

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