12-56752228-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000946.3(PRIM1):c.71C>G(p.Ser24Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000399 in 1,603,422 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000946.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152132Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000862 AC: 20AN: 232064Hom.: 0 AF XY: 0.0000478 AC XY: 6AN XY: 125468
GnomAD4 exome AF: 0.0000400 AC: 58AN: 1451290Hom.: 0 Cov.: 30 AF XY: 0.0000388 AC XY: 28AN XY: 720740
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152132Hom.: 0 Cov.: 30 AF XY: 0.0000673 AC XY: 5AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.71C>G (p.S24C) alteration is located in exon 1 (coding exon 1) of the PRIM1 gene. This alteration results from a C to G substitution at nucleotide position 71, causing the serine (S) at amino acid position 24 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at