15-64816348-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_001286496.2(PIF1):c.1876G>A(p.Asp626Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00217 in 1,614,058 control chromosomes in the GnomAD database, including 59 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001286496.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIF1 | ENST00000559239.2 | c.1876G>A | p.Asp626Asn | missense_variant | Exon 13 of 13 | 1 | NM_001286496.2 | ENSP00000452792.1 | ||
PIF1 | ENST00000268043.8 | c.1876G>A | p.Asp626Asn | missense_variant | Exon 13 of 13 | 1 | ENSP00000268043.4 | |||
PIF1 | ENST00000333425.10 | c.1866+226G>A | intron_variant | Intron 12 of 12 | 1 | ENSP00000328174.6 |
Frequencies
GnomAD3 genomes AF: 0.0110 AC: 1669AN: 152154Hom.: 37 Cov.: 33
GnomAD3 exomes AF: 0.00319 AC: 801AN: 251314Hom.: 13 AF XY: 0.00255 AC XY: 346AN XY: 135830
GnomAD4 exome AF: 0.00125 AC: 1834AN: 1461786Hom.: 22 Cov.: 35 AF XY: 0.00107 AC XY: 781AN XY: 727186
GnomAD4 genome AF: 0.0110 AC: 1675AN: 152272Hom.: 37 Cov.: 33 AF XY: 0.0108 AC XY: 805AN XY: 74440
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at