chr12-108562642-T-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_213595.4(ISCU):āc.20T>Gā(p.Phe7Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 1,469,126 control chromosomes in the GnomAD database, including 563,987 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F7G) has been classified as Benign.
Frequency
Consequence
NM_213595.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ISCU | NM_213595.4 | c.20T>G | p.Phe7Cys | missense_variant | 1/5 | ENST00000311893.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ISCU | ENST00000311893.14 | c.20T>G | p.Phe7Cys | missense_variant | 1/5 | 1 | NM_213595.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.865 AC: 131377AN: 151912Hom.: 56879 Cov.: 35
GnomAD3 exomes AF: 0.863 AC: 84642AN: 98032Hom.: 36707 AF XY: 0.865 AC XY: 49141AN XY: 56780
GnomAD4 exome AF: 0.877 AC: 1154731AN: 1317098Hom.: 507051 Cov.: 33 AF XY: 0.878 AC XY: 570016AN XY: 649158
GnomAD4 genome AF: 0.865 AC: 131493AN: 152028Hom.: 56936 Cov.: 35 AF XY: 0.865 AC XY: 64267AN XY: 74308
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 23, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 25, 2016 | - - |
Hereditary myopathy with lactic acidosis due to ISCU deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at