rs61743170
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The ENST00000420175.3(ASB10):c.798C>T(p.Ala266=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0551 in 1,613,038 control chromosomes in the GnomAD database, including 2,979 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.079 ( 614 hom., cov: 32)
Exomes 𝑓: 0.053 ( 2365 hom. )
Consequence
ASB10
ENST00000420175.3 synonymous
ENST00000420175.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.16
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 -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BP6
Variant 7-151181245-G-A is Benign according to our data. Variant chr7-151181245-G-A is described in ClinVar as [Benign]. Clinvar id is 677216.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-5.16 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ASB10 | NM_001142459.2 | c.798C>T | p.Ala266= | synonymous_variant | 3/6 | ENST00000420175.3 | NP_001135931.2 | |
ASB10 | NM_080871.4 | c.753C>T | p.Ala251= | synonymous_variant | 3/6 | NP_543147.2 | ||
ASB10 | NM_001142460.1 | c.798C>T | p.Ala266= | synonymous_variant | 3/5 | NP_001135932.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ASB10 | ENST00000420175.3 | c.798C>T | p.Ala266= | synonymous_variant | 3/6 | 1 | NM_001142459.2 | ENSP00000391137 | P4 | |
ASB10 | ENST00000275838.5 | c.798C>T | p.Ala266= | synonymous_variant | 3/5 | 1 | ENSP00000275838 | |||
ASB10 | ENST00000377867.7 | c.753C>T | p.Ala251= | synonymous_variant | 3/6 | 2 | ENSP00000367098 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0789 AC: 12006AN: 152144Hom.: 616 Cov.: 32
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GnomAD3 exomes AF: 0.0589 AC: 14623AN: 248462Hom.: 544 AF XY: 0.0572 AC XY: 7724AN XY: 135010
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GnomAD4 exome AF: 0.0526 AC: 76886AN: 1460776Hom.: 2365 Cov.: 34 AF XY: 0.0523 AC XY: 37982AN XY: 726728
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GnomAD4 genome AF: 0.0789 AC: 12010AN: 152262Hom.: 614 Cov.: 32 AF XY: 0.0775 AC XY: 5767AN XY: 74440
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 15, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 19, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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