7-151176244-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2

The NM_001142459.2(ASB10):c.1272G>A(p.Ser424Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0125 in 1,592,216 control chromosomes in the GnomAD database, including 193 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0082 ( 7 hom., cov: 33)

Exomes 𝑓: 0.013 ( 186 hom. )

Consequence

ASB10
NM_001142459.2 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4O:1

Conservation

PhyloP100: -2.12

Publications

3 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 -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.33).

BP6

Variant 7-151176244-C-T is Benign according to our data. Variant chr7-151176244-C-T is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 99951.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.12 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. GnomAdExome4 allele frequency = 0.0129 (18602/1439976) while in subpopulation NFE AF = 0.0157 (17280/1101966). AF 95% confidence interval is 0.0155. There are 186 homozygotes in GnomAdExome4. There are 8903 alleles in the male GnomAdExome4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High AC in GnomAd4 at 1248 AD,Unknown gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein
ASB10	NM_001142459.2 link	c.1272G>A	p.Ser424Ser	synonymous_variant	Exon 5 of 6	ENST00000420175.3	NP_001135931.2
ASB10	NM_080871.4 link	c.1227G>A	p.Ser409Ser	synonymous_variant	Exon 5 of 6		NP_543147.2
ASB10	NM_001142460.1 link	c.1158G>A	p.Ser386Ser	synonymous_variant	Exon 4 of 5		NP_001135932.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
ASB10	ENST00000420175.3 link	c.1272G>A	p.Ser424Ser	synonymous_variant	Exon 5 of 6	1	NM_001142459.2	ENSP00000391137.2
ASB10	ENST00000275838.5 link	c.1158G>A	p.Ser386Ser	synonymous_variant	Exon 4 of 5	1		ENSP00000275838.1
ASB10	ENST00000377867.7 link	c.1227G>A	p.Ser409Ser	synonymous_variant	Exon 5 of 6	2		ENSP00000367098.3

Frequencies

GnomAD3 genomes

AF:

0.00821

AC:

1249

AN:

152122

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00246

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.00681

Gnomad ASJ

AF:

0.00461

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000622

Gnomad FIN

AF:

0.000943

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0146

Gnomad OTH

AF:

0.00861

GnomAD2 exomes

AF:

0.00766

AC:

1752

AN:

228750

AF XY:

0.00755

show subpopulations

Gnomad AFR exome

AF:

0.00257

Gnomad AMR exome

AF:

0.00571

Gnomad ASJ exome

AF:

0.00490

Gnomad EAS exome

AF:

0.000113

Gnomad FIN exome

AF:

0.00176

Gnomad NFE exome

AF:

0.0134

Gnomad OTH exome

AF:

0.00905

GnomAD4 exome

AF:

0.0129

AC:

18602

AN:

1439976

Hom.:

186

Cov.:

AF XY:

0.0125

AC XY:

8903

AN XY:

714810

show subpopulations

African (AFR)

AF:

0.00235

AC:

AN:

32758

American (AMR)

AF:

0.00547

AC:

228

AN:

41690

Ashkenazi Jewish (ASJ)

AF:

0.00422

AC:

104

AN:

24658

East Asian (EAS)

AF:

0.0000507

AC:

AN:

39476

South Asian (SAS)

AF:

0.00107

AC:

AN:

83178

European-Finnish (FIN)

AF:

0.00234

AC:

121

AN:

51634

Middle Eastern (MID)

AF:

0.000966

AC:

AN:

5176

European-Non Finnish (NFE)

AF:

0.0157

AC:

17280

AN:

1101966

Other (OTH)

AF:

0.0117

AC:

696

AN:

59440

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

1181

2361

3542

4722

5903

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

656

1312

1968

2624

3280

<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:

0.00820

AC:

1248

AN:

152240

Hom.:

Cov.:

AF XY:

0.00709

AC XY:

528

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.00245

AC:

102

AN:

41554

American (AMR)

AF:

0.00673

AC:

103

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.00461

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5154

South Asian (SAS)

AF:

0.000622

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.000943

AC:

AN:

10608

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0146

AC:

990

AN:

68014

Other (OTH)

AF:

0.00852

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

139

208

278

347

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.0109

Hom.:

Bravo

AF:

0.00880

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

May 05, 2021

GeneDx

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Mar 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

ASB10: BP4, BP7, BS1, BS2 -

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Jan 13, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Glaucoma 1, open angle, F

Other:1

Casey Eye Institute Glaucoma Genetics Lab

Significance:not provided

Review Status:no classification provided

Collection Method:literature only

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Benign

0.89

(source)

DANN

Benign

0.90

PhyloP100

-2.1

Mutation Taster

=99/1

polymorphism

(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