chr4-102885281-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001008388.5(CISD2):c.169C>T(p.Arg57Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,788 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R57H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001008388.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CISD2 | NM_001008388.5 | c.169C>T | p.Arg57Cys | missense_variant | Exon 2 of 3 | ENST00000273986.10 | NP_001008389.1 | |
SLC9B1 | NM_001100874.3 | c.1380G>A | p.Thr460Thr | synonymous_variant | Exon 12 of 12 | NP_001094344.2 | ||
SLC9B1 | NR_047513.2 | n.1360G>A | non_coding_transcript_exon_variant | Exon 11 of 11 | ||||
SLC9B1 | NR_047515.2 | n.1222G>A | non_coding_transcript_exon_variant | Exon 11 of 11 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251384Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135868
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461788Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727186
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Wolfram syndrome 2 Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at