rs61734407
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001142459.2(ASB10):c.1024C>T(p.Leu342=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00524 in 1,606,700 control chromosomes in the GnomAD database, including 68 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0040 ( 6 hom., cov: 33)
Exomes 𝑓: 0.0054 ( 62 hom. )
Consequence
ASB10
NM_001142459.2 synonymous
NM_001142459.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.341
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 7-151181019-G-A is Benign according to our data. Variant chr7-151181019-G-A is described in ClinVar as [Benign]. Clinvar id is 99990.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.341 with no splicing effect.
BS2
?
High AC in GnomAd4 at 603 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASB10 | NM_001142459.2 | c.1024C>T | p.Leu342= | synonymous_variant | 3/6 | ENST00000420175.3 | |
ASB10 | NM_080871.4 | c.979C>T | p.Leu327= | synonymous_variant | 3/6 | ||
ASB10 | NM_001142460.1 | c.1024C>T | p.Leu342= | synonymous_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASB10 | ENST00000420175.3 | c.1024C>T | p.Leu342= | synonymous_variant | 3/6 | 1 | NM_001142459.2 | P4 | |
ASB10 | ENST00000275838.5 | c.1024C>T | p.Leu342= | synonymous_variant | 3/5 | 1 | |||
ASB10 | ENST00000377867.7 | c.979C>T | p.Leu327= | synonymous_variant | 3/6 | 2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00397 AC: 604AN: 152244Hom.: 6 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00510 AC: 1240AN: 243130Hom.: 13 AF XY: 0.00525 AC XY: 698AN XY: 132902
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GnomAD4 exome AF: 0.00538 AC: 7818AN: 1454338Hom.: 62 Cov.: 31 AF XY: 0.00538 AC XY: 3889AN XY: 722258
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GnomAD4 genome ? AF: 0.00396 AC: 603AN: 152362Hom.: 6 Cov.: 33 AF XY: 0.00382 AC XY: 285AN XY: 74516
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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 submitter | clinical testing | Invitae | Nov 06, 2023 | - - |
Glaucoma 1, open angle, F Other:1
not provided, no classification provided | literature only | Casey Eye Institute Glaucoma Genetics Lab | - | - - |
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