chr1-25984487-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_000437.4(PAFAH2):c.383G>A(p.Gly128Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0000205 in 1,461,640 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 (★).
Frequency
Consequence
NM_000437.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250584Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135490
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461640Hom.: 0 Cov.: 30 AF XY: 0.0000303 AC XY: 22AN XY: 727118
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.383G>A (p.G128D) alteration is located in exon 5 (coding exon 4) of the PAFAH2 gene. This alteration results from a G to A substitution at nucleotide position 383, causing the glycine (G) at amino acid position 128 to be replaced by an aspartic acid (D). 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