rs104886473
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001142459.2(ASB10):c.565C>T(p.Arg189Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000958 in 1,587,348 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001142459.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASB10 | NM_001142459.2 | c.565C>T | p.Arg189Trp | missense_variant | 2/6 | ENST00000420175.3 | |
ASB10 | NM_080871.4 | c.520C>T | p.Arg174Trp | missense_variant | 2/6 | ||
ASB10 | NM_001142460.1 | c.565C>T | p.Arg189Trp | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASB10 | ENST00000420175.3 | c.565C>T | p.Arg189Trp | missense_variant | 2/6 | 1 | NM_001142459.2 | P4 | |
ASB10 | ENST00000275838.5 | c.565C>T | p.Arg189Trp | missense_variant | 2/5 | 1 | |||
ASB10 | ENST00000377867.7 | c.520C>T | p.Arg174Trp | missense_variant | 2/6 | 2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000743 AC: 113AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000998 AC: 201AN: 201474Hom.: 1 AF XY: 0.00102 AC XY: 111AN XY: 108824
GnomAD4 exome AF: 0.000981 AC: 1408AN: 1435050Hom.: 2 Cov.: 31 AF XY: 0.00106 AC XY: 752AN XY: 711338
GnomAD4 genome ? AF: 0.000742 AC: 113AN: 152298Hom.: 0 Cov.: 33 AF XY: 0.000672 AC XY: 50AN XY: 74452
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 17, 2022 | - - |
Glaucoma 1, open angle, F Other:1
not provided, no classification provided | literature only | Casey Eye Institute Glaucoma Genetics Lab | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at