rs151344613
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BS2_Supporting
The NM_001142459.2(ASB10):c.628C>T(p.Arg210Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,608,814 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
ASB10
NM_001142459.2 missense
NM_001142459.2 missense
Scores
1
8
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.59
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 Likely_benign. Variant got -1 ACMG points.
BS2
High AC in GnomAd4 at 6 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ASB10 | NM_001142459.2 | c.628C>T | p.Arg210Trp | missense_variant | 3/6 | ENST00000420175.3 | NP_001135931.2 | |
ASB10 | NM_080871.4 | c.583C>T | p.Arg195Trp | missense_variant | 3/6 | NP_543147.2 | ||
ASB10 | NM_001142460.1 | c.628C>T | p.Arg210Trp | missense_variant | 3/5 | NP_001135932.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ASB10 | ENST00000420175.3 | c.628C>T | p.Arg210Trp | missense_variant | 3/6 | 1 | NM_001142459.2 | ENSP00000391137.2 | ||
ASB10 | ENST00000275838.5 | c.628C>T | p.Arg210Trp | missense_variant | 3/5 | 1 | ENSP00000275838.1 | |||
ASB10 | ENST00000377867.7 | c.583C>T | p.Arg195Trp | missense_variant | 3/6 | 2 | ENSP00000367098.3 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152072Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000205 AC: 5AN: 244464Hom.: 0 AF XY: 0.0000225 AC XY: 3AN XY: 133342
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GnomAD4 exome AF: 0.0000227 AC: 33AN: 1456742Hom.: 0 Cov.: 34 AF XY: 0.0000207 AC XY: 15AN XY: 723948
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GnomAD4 genome AF: 0.0000395 AC: 6AN: 152072Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74268
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Pathogenic
DEOGEN2
Benign
.;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;.;M
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D
REVEL
Benign
Sift
Benign
D;D;D
Sift4G
Uncertain
T;T;T
Polyphen
1.0
.;D;D
Vest4
MVP
MPC
0.25
ClinPred
D
GERP RS
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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