rs61743170

Variant names:

• chr7-151181245-G-A
• rs61743170
• NM_001142459.2:c.798C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-151181245-G-A
• chr7-151181245-G-C

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_001142459.2(ASB10):​c.798C>T​(p.Ala266Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0551 in 1,613,038 control chromosomes in the GnomAD database, including 2,979 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.079 (614 hom., cov: 32)
  • Exomes 𝑓: 0.053 (2365 hom.)
• Consequence: ASB10 NM_001142459.2 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -5.16
• Publications: 6 publications found

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 Gene-Disease associations (from GenCC):

• glaucoma 1, open angle, F

  Inheritance: AD, Unknown Classification: LIMITED Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 7-151181245-G-A is Benign according to our data. Variant chr7-151181245-G-A is described in ClinVar as [Benign]. Clinvar id is 677216.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-5.16 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASB10	NM_001142459.2	c.798C>T	p.Ala266Ala	synonymous_variant	Exon 3 of 6	ENST00000420175.3	NP_001135931.2
ASB10	NM_080871.4	c.753C>T	p.Ala251Ala	synonymous_variant	Exon 3 of 6		NP_543147.2
ASB10	NM_001142460.1	c.798C>T	p.Ala266Ala	synonymous_variant	Exon 3 of 5		NP_001135932.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASB10	ENST00000420175.3	c.798C>T	p.Ala266Ala	synonymous_variant	Exon 3 of 6	1	NM_001142459.2	ENSP00000391137.2
ASB10	ENST00000275838.5	c.798C>T	p.Ala266Ala	synonymous_variant	Exon 3 of 5	1		ENSP00000275838.1
ASB10	ENST00000377867.7	c.753C>T	p.Ala251Ala	synonymous_variant	Exon 3 of 6	2		ENSP00000367098.3

Frequencies

GnomAD3 genomes AF: 0.0789 AC: 12006 AN: 152144 Hom.: 616 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0567

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.0801

Gnomad SAS AF: 0.0421

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0503

Gnomad OTH AF: 0.0824

GnomAD2 exomes AF: 0.0589 AC: 14623 AN: 248462 AF XY: 0.0572

Gnomad AFR exome AF: 0.150

Gnomad AMR exome AF: 0.0339

Gnomad ASJ exome AF: 0.0676

Gnomad EAS exome AF: 0.0797

Gnomad FIN exome AF: 0.0651

Gnomad NFE exome AF: 0.0534

Gnomad OTH exome AF: 0.0563

GnomAD4 exome AF: 0.0526 AC: 76886 AN: 1460776 Hom.: 2365 Cov.: 34 AF XY: 0.0523 AC XY: 37982 AN XY: 726728

African (AFR) AF: 0.151 AC: 5043 AN: 33478

American (AMR) AF: 0.0359 AC: 1605 AN: 44710

Ashkenazi Jewish (ASJ) AF: 0.0671 AC: 1753 AN: 26118

East Asian (EAS) AF: 0.0705 AC: 2797 AN: 39694

South Asian (SAS) AF: 0.0416 AC: 3587 AN: 86248

European-Finnish (FIN) AF: 0.0656 AC: 3440 AN: 52444

Middle Eastern (MID) AF: 0.0652 AC: 376 AN: 5768

European-Non Finnish (NFE) AF: 0.0490 AC: 54503 AN: 1111936

Other (OTH) AF: 0.0626 AC: 3782 AN: 60380

GnomAD4 genome AF: 0.0789 AC: 12010 AN: 152262 Hom.: 614 Cov.: 32 AF XY: 0.0775 AC XY: 5767 AN XY: 74440

African (AFR) AF: 0.144 AC: 5971 AN: 41538

American (AMR) AF: 0.0566 AC: 866 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0677 AC: 235 AN: 3472

East Asian (EAS) AF: 0.0799 AC: 413 AN: 5172

South Asian (SAS) AF: 0.0423 AC: 204 AN: 4820

European-Finnish (FIN) AF: 0.0659 AC: 700 AN: 10618

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0503 AC: 3422 AN: 68026

Other (OTH) AF: 0.0815 AC: 172 AN: 2110

Alfa AF: 0.0552 Hom.: 160

Bravo AF: 0.0816

Asia WGS AF: 0.0570 AC: 196 AN: 3478

EpiCase AF: 0.0541

EpiControl AF: 0.0557

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:3

Jan 20, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 19, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.028
DANN	Benign	0.53
PhyloP100		-5.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs61743170; hg19: chr7-150878332;