rs35405862
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_033109.5(PNPT1):āc.944A>Gā(p.Lys315Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000784 in 1,542,178 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_033109.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PNPT1 | NM_033109.5 | c.944A>G | p.Lys315Arg | missense_variant | Exon 11 of 28 | ENST00000447944.7 | NP_149100.2 | |
PNPT1 | XM_005264629.3 | c.704A>G | p.Lys235Arg | missense_variant | Exon 11 of 28 | XP_005264686.1 | ||
PNPT1 | XM_017005172.2 | c.704A>G | p.Lys235Arg | missense_variant | Exon 10 of 27 | XP_016860661.1 | ||
PNPT1 | XM_047446161.1 | c.944A>G | p.Lys315Arg | missense_variant | Exon 11 of 20 | XP_047302117.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00451 AC: 686AN: 152224Hom.: 9 Cov.: 33
GnomAD3 exomes AF: 0.00100 AC: 216AN: 215022Hom.: 1 AF XY: 0.000716 AC XY: 84AN XY: 117342
GnomAD4 exome AF: 0.000373 AC: 519AN: 1389836Hom.: 6 Cov.: 26 AF XY: 0.000311 AC XY: 215AN XY: 691080
GnomAD4 genome AF: 0.00453 AC: 690AN: 152342Hom.: 9 Cov.: 33 AF XY: 0.00411 AC XY: 306AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
PNPT1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at