19-42297326-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_002573.4(PAFAH1B3):c.448G>A(p.Glu150Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,612,792 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E150V) 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAFAH1B3 | NM_002573.4 | c.448G>A | p.Glu150Lys | missense_variant | Exon 5 of 5 | ENST00000262890.8 | NP_002564.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250506Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135528
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460616Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726348
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.448G>A (p.E150K) 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 448, causing the glutamic acid (E) at amino acid position 150 to be replaced by a lysine (K). 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