rs77615410

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001142459.2(ASB10):c.470C>T(p.Ala157Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0108 in 1,602,050 control chromosomes in the GnomAD database, including 1,301 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.022 ( 177 hom., cov: 33)

Exomes 𝑓: 0.0096 ( 1124 hom. )

Consequence

ASB10
NM_001142459.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3O:1

Conservation

PhyloP100: 1.87

Publications

6 publications found

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 Gene-Disease associations (from GenCC):

glaucoma 1, open angle, F
Inheritance: Unknown, AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), ClinGen

ASB10 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004033804).

BP6

Variant 7-151186506-G-A is Benign according to our data. Variant chr7-151186506-G-A is described in ClinVar as Benign. ClinVar VariationId is 99955.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142459.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ASB10	NM_001142459.2	MANE Select	c.470C>T	p.Ala157Val	missense	Exon 2 of 6	NP_001135931.2	Q8WXI3-1
ASB10	NM_080871.4		c.425C>T	p.Ala142Val	missense	Exon 2 of 6	NP_543147.2	Q8WXI3-3
ASB10	NM_001142460.1		c.470C>T	p.Ala157Val	missense	Exon 2 of 5	NP_001135932.2	Q8WXI3-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ASB10	ENST00000420175.3	TSL:1 MANE Select	c.470C>T	p.Ala157Val	missense	Exon 2 of 6	ENSP00000391137.2	Q8WXI3-1
ASB10	ENST00000275838.5	TSL:1	c.470C>T	p.Ala157Val	missense	Exon 2 of 5	ENSP00000275838.1	Q8WXI3-2
ASB10	ENST00000968508.1		c.470C>T	p.Ala157Val	missense	Exon 2 of 6	ENSP00000638567.1

Frequencies

GnomAD3 genomes

AF:

0.0221

AC:

3358

AN:

152214

Hom.:

179

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0399

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0211

Gnomad ASJ

AF:

0.00951

Gnomad EAS

AF:

0.234

Gnomad SAS

AF:

0.0116

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000661

Gnomad OTH

AF:

0.0167

GnomAD2 exomes

AF:

0.0279

AC:

6243

AN:

224016

AF XY:

0.0248

show subpopulations

Gnomad AFR exome

AF:

0.0392

Gnomad AMR exome

AF:

0.0434

Gnomad ASJ exome

AF:

0.00863

Gnomad EAS exome

AF:

0.239

Gnomad FIN exome

AF:

0.000371

Gnomad NFE exome

AF:

0.000744

Gnomad OTH exome

AF:

0.0153

GnomAD4 exome

AF:

0.00958

AC:

13885

AN:

1449718

Hom.:

1124

Cov.:

AF XY:

0.00929

AC XY:

6694

AN XY:

720212

show subpopulations

African (AFR)

AF:

0.0382

AC:

1270

AN:

33254

American (AMR)

AF:

0.0412

AC:

1768

AN:

42898

Ashkenazi Jewish (ASJ)

AF:

0.00696

AC:

180

AN:

25854

East Asian (EAS)

AF:

0.223

AC:

8684

AN:

39006

South Asian (SAS)

AF:

0.00551

AC:

465

AN:

84444

European-Finnish (FIN)

AF:

0.000212

AC:

AN:

51890

Middle Eastern (MID)

AF:

0.00645

AC:

AN:

5732

European-Non Finnish (NFE)

AF:

0.000345

AC:

382

AN:

1106764

Other (OTH)

AF:

0.0182

AC:

1088

AN:

59876

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

757

1514

2272

3029

3786

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

210

420

630

840

1050

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0221

AC:

3363

AN:

152332

Hom.:

177

Cov.:

AF XY:

0.0226

AC XY:

1685

AN XY:

74492

show subpopulations

African (AFR)

AF:

0.0399

AC:

1658

AN:

41576

American (AMR)

AF:

0.0211

AC:

323

AN:

15312

Ashkenazi Jewish (ASJ)

AF:

0.00951

AC:

AN:

3470

East Asian (EAS)

AF:

0.233

AC:

1207

AN:

5172

South Asian (SAS)

AF:

0.0122

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10628

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000662

AC:

AN:

68022

Other (OTH)

AF:

0.0170

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

157

314

472

629

786

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

176

220

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0121

Hom.:

207

Bravo

AF:

0.0256

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.0398

AC:

175

ESP6500EA

AF:

0.00151

AC:

ExAC

AF:

0.0247

AC:

2986

Asia WGS

AF:

0.0990

AC:

342

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

Glaucoma 1, open angle, F (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.076

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.55

CADD

Benign

(source)

DANN

Benign

0.97

DEOGEN2

Benign

0.015

Eigen

Benign

-0.90

Eigen_PC

Benign

-0.89

FATHMM_MKL

Benign

0.28

LIST_S2

Benign

0.81

MetaRNN

Benign

0.0040

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.3

PhyloP100

1.9

PrimateAI

Benign

0.40

PROVEAN

Benign

-1.6

REVEL

Benign

0.048

Sift

Benign

0.26

Sift4G

Benign

0.33

Polyphen

0.0010

Vest4

0.14

MPC

0.051

ClinPred

0.0023

GERP RS

2.5

Varity_R

0.067

gMVP

0.23

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over