Variant 7-151187667-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_080871.4(ASB10):c.56C>G(p.Pro19Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00386 in 1,513,956 control chromosomes in the GnomAD database, including 180 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P19S) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.019 ( 100 hom., cov: 32)

Exomes 𝑓: 0.0021 ( 80 hom. )

Consequence

ASB10
NM_080871.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1O:1

Conservation

PhyloP100: -0.0470

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0022161305).

BP6

Variant 7-151187667-G-C is Benign according to our data. Variant chr7-151187667-G-C is described in ClinVar as [Benign]. Clinvar id is 99961.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASB10	NM_080871.4 linkuse as main transcript	c.56C>G	p.Pro19Arg	missense_variant	1/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASB10	ENST00000377867.7 linkuse as main transcript	c.56C>G	p.Pro19Arg	missense_variant	1/6	2		A1	Q8WXI3-3
ASB10	ENST00000415615.1 linkuse as main transcript	c.56C>G	p.Pro19Arg	missense_variant, NMD_transcript_variant	1/3	4

Frequencies

GnomAD3 genomes

AF:

0.0194

AC:

2958

AN:

152156

Hom.:

100

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0664

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00850

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000515

Gnomad OTH

AF:

0.0163

GnomAD3 exomes

AF:

0.00534

AC:

681

AN:

127568

Hom.:

AF XY:

0.00421

AC XY:

277

AN XY:

65856

show subpopulations

Gnomad AFR exome

AF:

0.0698

Gnomad AMR exome

AF:

0.00493

Gnomad ASJ exome

AF:

0.000181

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000120

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000396

Gnomad OTH exome

AF:

0.00305

GnomAD4 exome

AF:

0.00212

AC:

2893

AN:

1361682

Hom.:

Cov.:

AF XY:

0.00186

AC XY:

1236

AN XY:

665822

show subpopulations

Gnomad4 AFR exome

AF:

0.0682

Gnomad4 AMR exome

AF:

0.00552

Gnomad4 ASJ exome

AF:

0.000265

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000108

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000327

Gnomad4 OTH exome

AF:

0.00395

GnomAD4 genome

AF:

0.0194

AC:

2955

AN:

152274

Hom.:

100

Cov.:

AF XY:

0.0189

AC XY:

1405

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.0662

Gnomad4 AMR

AF:

0.00849

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000515

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.00335

Hom.:

Bravo

AF:

0.0229

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.000519

AC:

ESP6500AA

AF:

0.0723

AC:

100

ESP6500EA

AF:

0.000629

AC:

ExAC

AF:

0.00580

AC:

158

Asia WGS

AF:

0.00202

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1Other:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 17, 2019

This variant is associated with the following publications: (PMID: 22798626) -

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_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.45

Cadd

Benign

4.7

Dann

Uncertain

1.0

Eigen

Benign

-0.72

Eigen_PC

Benign

-0.75

FATHMM_MKL

Benign

0.072

LIST_S2

Benign

0.40

MetaRNN

Benign

0.0022

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

PROVEAN

Benign

-1.0

REVEL

Benign

0.072

Sift

Benign

0.092

Sift4G

Benign

0.077

Polyphen

0.0060

Vest4

0.21

MVP

0.22

ClinPred

0.0059

GERP RS

3.7

Splicing

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