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rs104886471

chr7-151186460-G-Achr7-151186460-G-C

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001142459.2(ASB10):c.516C>T(p.Ala172=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000166 in 1,594,058 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00079 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00010 ( 1 hom. )

Consequence

ASB10
NM_001142459.2 synonymous

Scores

2

Clinical Significance

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

Conservation

PhyloP100: -1.24
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-151186460-G-A is Benign according to our data. Variant chr7-151186460-G-A is described in ClinVar as [Benign]. Clinvar id is 99957.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.24 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 120 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ASB10NM_001142459.2 linkuse as main transcriptc.516C>T p.Ala172= synonymous_variant 2/6 ENST00000420175.3
ASB10NM_080871.4 linkuse as main transcriptc.471C>T p.Ala157= synonymous_variant 2/6
ASB10NM_001142460.1 linkuse as main transcriptc.516C>T p.Ala172= synonymous_variant 2/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ASB10ENST00000420175.3 linkuse as main transcriptc.516C>T p.Ala172= synonymous_variant 2/61 NM_001142459.2 P4Q8WXI3-1
ASB10ENST00000275838.5 linkuse as main transcriptc.516C>T p.Ala172= synonymous_variant 2/51 Q8WXI3-2
ASB10ENST00000377867.7 linkuse as main transcriptc.471C>T p.Ala157= synonymous_variant 2/62 A1Q8WXI3-3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000788
AC:
120
AN:
152196
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00280
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000196
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.000218
AC:
46
AN:
210914
Hom.:
0
AF XY:
0.000149
AC XY:
17
AN XY:
114314
show subpopulations
Gnomad AFR exome
AF:
0.00262
Gnomad AMR exome
AF:
0.0000326
Gnomad ASJ exome
AF:
0.000216
Gnomad EAS exome
AF:
0.000384
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000324
Gnomad OTH exome
AF:
0.000189
GnomAD4 exome
AF:
0.0000999
AC:
144
AN:
1441744
Hom.:
1
Cov.:
31
AF XY:
0.0000880
AC XY:
63
AN XY:
715508
show subpopulations
Gnomad4 AFR exome
AF:
0.00308
Gnomad4 AMR exome
AF:
0.0000721
Gnomad4 ASJ exome
AF:
0.0000778
Gnomad4 EAS exome
AF:
0.000311
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000907
Gnomad4 OTH exome
AF:
0.000251
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000788
AC:
120
AN:
152314
Hom.:
0
Cov.:
33
AF XY:
0.000806
AC XY:
60
AN XY:
74470
show subpopulations
Gnomad4 AFR
AF:
0.00279
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.000558
Hom.:
0
Bravo
AF:
0.000873

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 submitterclinical testingInvitaeDec 06, 2022- -
Glaucoma 1, open angle, F Other:1
not provided, no classification providedliterature onlyCasey Eye Institute Glaucoma Genetics Lab -- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
Cadd
Benign
0.17
Dann
Benign
0.86

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs104886471; hg19: chr7-150883547; COSMIC: COSV51995357; COSMIC: COSV51995357; API