rs140602973
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001142459.2(ASB10):c.815G>A(p.Arg272His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000215 in 1,612,814 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: 𝑓 0.00039 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00020 ( 0 hom. )
Consequence
ASB10
NM_001142459.2 missense
NM_001142459.2 missense
Scores
3
15
Clinical Significance
Conservation
PhyloP100: 1.47
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.011714309).
BS2
?
High AC in GnomAd4 at 60 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASB10 | NM_001142459.2 | c.815G>A | p.Arg272His | missense_variant | 3/6 | ENST00000420175.3 | |
ASB10 | NM_080871.4 | c.770G>A | p.Arg257His | missense_variant | 3/6 | ||
ASB10 | NM_001142460.1 | c.815G>A | p.Arg272His | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASB10 | ENST00000420175.3 | c.815G>A | p.Arg272His | missense_variant | 3/6 | 1 | NM_001142459.2 | P4 | |
ASB10 | ENST00000275838.5 | c.815G>A | p.Arg272His | missense_variant | 3/5 | 1 | |||
ASB10 | ENST00000377867.7 | c.770G>A | p.Arg257His | missense_variant | 3/6 | 2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000394 AC: 60AN: 152214Hom.: 1 Cov.: 32
GnomAD3 genomes
?
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32
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GnomAD3 exomes AF: 0.000311 AC: 77AN: 247744Hom.: 0 AF XY: 0.000304 AC XY: 41AN XY: 134746
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GnomAD4 exome AF: 0.000196 AC: 287AN: 1460600Hom.: 0 Cov.: 34 AF XY: 0.000168 AC XY: 122AN XY: 726626
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GnomAD4 genome ? AF: 0.000394 AC: 60AN: 152214Hom.: 1 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74370
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ExAC
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ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
Glaucoma 1, open angle, F Other:1
not provided, no classification provided | literature only | Casey Eye Institute Glaucoma Genetics Lab | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;L
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Benign
T;T;T
Polyphen
0.57, 0.69
.;P;P
Vest4
MVP
MPC
0.069
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at