NM_001142459.2:c.1114C>T

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.1114C>T(p.Arg372Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0545 in 1,550,106 control chromosomes in the GnomAD database, including 2,567 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.068 ( 402 hom., cov: 32)

Exomes 𝑓: 0.053 ( 2165 hom. )

Consequence

ASB10
NM_001142459.2 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 4.10

Publications

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

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=0.003540486).

BP6

Variant 7-151176667-G-A is Benign according to our data. Variant chr7-151176667-G-A is described in ClinVar as Benign. ClinVar VariationId is 677160.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein
ASB10	NM_001142459.2 link	c.1114C>T	p.Arg372Cys	missense_variant	Exon 4 of 6	ENST00000420175.3	NP_001135931.2
ASB10	NM_080871.4 link	c.1069C>T	p.Arg357Cys	missense_variant	Exon 4 of 6		NP_543147.2
ASB10	NM_001142460.1 link	c.1105-370C>T		intron_variant	Intron 3 of 4		NP_001135932.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
ASB10	ENST00000420175.3 link	c.1114C>T	p.Arg372Cys	missense_variant	Exon 4 of 6	1	NM_001142459.2	ENSP00000391137.2
ASB10	ENST00000275838.5 link	c.1105-370C>T		intron_variant	Intron 3 of 4	1		ENSP00000275838.1
ASB10	ENST00000377867.7 link	c.1069C>T	p.Arg357Cys	missense_variant	Exon 4 of 6	2		ENSP00000367098.3

Frequencies

GnomAD3 genomes

AF:

0.0675

AC:

10272

AN:

152074

Hom.:

402

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0976

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.0490

Gnomad ASJ

AF:

0.0677

Gnomad EAS

AF:

0.0848

Gnomad SAS

AF:

0.0381

Gnomad FIN

AF:

0.0789

Gnomad MID

AF:

0.0545

Gnomad NFE

AF:

0.0530

Gnomad OTH

AF:

0.0745

GnomAD2 exomes

AF:

0.0553

AC:

8685

AN:

156914

AF XY:

0.0545

show subpopulations

Gnomad AFR exome

AF:

0.0971

Gnomad AMR exome

AF:

0.0311

Gnomad ASJ exome

AF:

0.0653

Gnomad EAS exome

AF:

0.0857

Gnomad FIN exome

AF:

0.0776

Gnomad NFE exome

AF:

0.0549

Gnomad OTH exome

AF:

0.0574

GnomAD4 exome

AF:

0.0531

AC:

74187

AN:

1397912

Hom.:

2165

Cov.:

AF XY:

0.0528

AC XY:

36388

AN XY:

689398

show subpopulations

African (AFR)

AF:

0.0953

AC:

3007

AN:

31556

American (AMR)

AF:

0.0332

AC:

1185

AN:

35686

Ashkenazi Jewish (ASJ)

AF:

0.0668

AC:

1680

AN:

25166

East Asian (EAS)

AF:

0.0744

AC:

2656

AN:

35708

South Asian (SAS)

AF:

0.0355

AC:

2816

AN:

79220

European-Finnish (FIN)

AF:

0.0776

AC:

3806

AN:

49020

Middle Eastern (MID)

AF:

0.0662

AC:

376

AN:

5682

European-Non Finnish (NFE)

AF:

0.0512

AC:

55164

AN:

1077886

Other (OTH)

AF:

0.0603

AC:

3497

AN:

57988

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

3502

7004

10507

14009

17511

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2098

4196

6294

8392

10490

<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:

0.0675

AC:

10276

AN:

152194

Hom.:

402

Cov.:

AF XY:

0.0680

AC XY:

5059

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.0976

AC:

4049

AN:

41500

American (AMR)

AF:

0.0490

AC:

749

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0677

AC:

235

AN:

3472

East Asian (EAS)

AF:

0.0846

AC:

437

AN:

5164

South Asian (SAS)

AF:

0.0381

AC:

184

AN:

4826

European-Finnish (FIN)

AF:

0.0789

AC:

837

AN:

10602

Middle Eastern (MID)

AF:

0.0479

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0530

AC:

3605

AN:

68012

Other (OTH)

AF:

0.0737

AC:

156

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

491

982

1473

1964

2455

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

240

360

480

600

<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:

0.0586

Hom.:

988

Bravo

AF:

0.0670

TwinsUK

AF:

0.0467

AC:

173

ALSPAC

AF:

0.0537

AC:

207

ExAC

AF:

0.0498

AC:

1342

Asia WGS

AF:

0.0550

AC:

190

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

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

AlphaMissense

Benign

0.25

BayesDel_addAF

Benign

-0.32

BayesDel_noAF

Benign

-0.16

CADD

Pathogenic

(source)

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.012

.;T

Eigen

Uncertain

0.31

Eigen_PC

Uncertain

0.32

FATHMM_MKL

Benign

0.68

LIST_S2

Uncertain

0.88

D;D

MetaRNN

Benign

0.0035

T;T

MetaSVM

Benign

-0.86

MutationAssessor

Benign

1.6

.;L

PhyloP100

4.1

PrimateAI

Uncertain

0.56

PROVEAN

Benign

-0.67

N;N

REVEL

Benign

0.27

Sift

Benign

0.18

T;T

Sift4G

Benign

0.18

T;T

Polyphen

0.49

P;D

Vest4

0.23

MPC

0.066

ClinPred

0.010

GERP RS

4.5

Varity_R

0.084

gMVP

0.44

Mutation Taster

=95/5

polymorphism (auto)

(source)

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

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over