12-56934048-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_148897.3(SDR9C7):c.214C>T(p.Arg72Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,614,180 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R72Q) has been classified as Likely benign.
Frequency
Consequence
NM_148897.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDR9C7 | NM_148897.3 | c.214C>T | p.Arg72Trp | missense_variant | 1/4 | ENST00000293502.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDR9C7 | ENST00000293502.2 | c.214C>T | p.Arg72Trp | missense_variant | 1/4 | 1 | NM_148897.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251226Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135772
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461876Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727242
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152304Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74482
ClinVar
Submissions by phenotype
Ichthyosis, congenital, autosomal recessive 13 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 14, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at