chr19-42297157-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002573.4(PAFAH1B3):c.617G>A(p.Arg206Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000171 in 1,613,786 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign 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. R206W) has been classified as Uncertain significance.
Frequency
Consequence
NM_002573.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAFAH1B3 | NM_002573.4 | c.617G>A | p.Arg206Gln | missense_variant | Exon 5 of 5 | ENST00000262890.8 | NP_002564.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251348Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135856
GnomAD4 exome AF: 0.000172 AC: 251AN: 1461610Hom.: 0 Cov.: 31 AF XY: 0.000175 AC XY: 127AN XY: 727044
GnomAD4 genome AF: 0.000164 AC: 25AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.617G>A (p.R206Q) alteration is located in exon 6 (coding exon 5) of the PAFAH1B3 gene. This alteration results from a G to A substitution at nucleotide position 617, causing the arginine (R) at amino acid position 206 to be replaced by a glutamine (Q). 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