20-13270678-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_080826.2(ISM1):c.313C>T(p.Leu105Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00126 in 1,613,910 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_080826.2 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 |
---|---|---|---|---|---|---|---|
ISM1 | NM_080826.2 | c.313C>T | p.Leu105Phe | missense_variant | 2/6 | ENST00000262487.5 | |
ISM1 | XM_017027680.2 | c.313C>T | p.Leu105Phe | missense_variant | 2/7 | ||
TASP1 | XR_001754319.3 | n.1369+45292G>A | intron_variant, non_coding_transcript_variant | ||||
TASP1 | XR_007067463.1 | n.1370-4496G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ISM1 | ENST00000262487.5 | c.313C>T | p.Leu105Phe | missense_variant | 2/6 | 5 | NM_080826.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00289 AC: 440AN: 152180Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00177 AC: 441AN: 249164Hom.: 5 AF XY: 0.00163 AC XY: 220AN XY: 135180
GnomAD4 exome AF: 0.00109 AC: 1600AN: 1461612Hom.: 7 Cov.: 32 AF XY: 0.00108 AC XY: 786AN XY: 727100
GnomAD4 genome ? AF: 0.00286 AC: 436AN: 152298Hom.: 4 Cov.: 33 AF XY: 0.00290 AC XY: 216AN XY: 74474
ClinVar
Submissions by phenotype
ISM1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 26, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at