dbSNP rs2257073: ASB10:c.584+192G>A (chr7-151186200-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001142459.2(ASB10):c.584+192G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,106 control chromosomes in the GnomAD database, including 5,132 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 5132 hom., cov: 32)

Consequence

ASB10
NM_001142459.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.162

Publications

1 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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 7-151186200-C-T is Benign according to our data. Variant chr7-151186200-C-T is described in ClinVar as Benign. ClinVar VariationId is 1248058.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 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	Effect	Exon Rank	Protein	UniProt
ASB10	NM_001142459.2	MANE Select	c.584+192G>A	intron	N/A	NP_001135931.2	Q8WXI3-1
ASB10	NM_080871.4		c.539+192G>A	intron	N/A	NP_543147.2	Q8WXI3-3
ASB10	NM_001142460.1		c.584+192G>A	intron	N/A	NP_001135932.2	Q8WXI3-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ASB10	ENST00000420175.3	TSL:1 MANE Select	c.584+192G>A	intron	N/A	ENSP00000391137.2	Q8WXI3-1
ASB10	ENST00000275838.5	TSL:1	c.584+192G>A	intron	N/A	ENSP00000275838.1	Q8WXI3-2
ASB10	ENST00000968508.1		c.584+192G>A	intron	N/A	ENSP00000638567.1

Frequencies

GnomAD3 genomes

AF:

0.257

AC:

39027

AN:

151988

Hom.:

5130

Cov.:

show subpopulations

Gnomad AFR

AF:

0.248

Gnomad AMI

AF:

0.281

Gnomad AMR

AF:

0.250

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.102

Gnomad SAS

AF:

0.205

Gnomad FIN

AF:

0.221

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.279

Gnomad OTH

AF:

0.281

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.257

AC:

39051

AN:

152106

Hom.:

5132

Cov.:

AF XY:

0.251

AC XY:

18670

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.248

AC:

10296

AN:

41478

American (AMR)

AF:

0.249

AC:

3807

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.358

AC:

1243

AN:

3468

East Asian (EAS)

AF:

0.102

AC:

528

AN:

5178

South Asian (SAS)

AF:

0.205

AC:

990

AN:

4818

European-Finnish (FIN)

AF:

0.221

AC:

2337

AN:

10594

Middle Eastern (MID)

AF:

0.245

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.279

AC:

18931

AN:

67972

Other (OTH)

AF:

0.281

AC:

592

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1501

3002

4504

6005

7506

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<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:

0.269

Hom.:

3050

Bravo

AF:

0.259

Asia WGS

AF:

0.162

AC:

564

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.7

(source)

DANN

Benign

0.60

PhyloP100

0.16

Mutation Taster

=100/0

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over