3-122699935-A-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_017554.3(PARP14):c.1381A>G(p.Lys461Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017554.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PARP14 | NM_017554.3 | c.1381A>G | p.Lys461Glu | missense_variant | 6/17 | ENST00000474629.7 | |
PARP14 | XM_011512929.3 | c.1381A>G | p.Lys461Glu | missense_variant | 6/10 | ||
PARP14 | XR_007095695.1 | n.1426A>G | non_coding_transcript_exon_variant | 6/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PARP14 | ENST00000474629.7 | c.1381A>G | p.Lys461Glu | missense_variant | 6/17 | 1 | NM_017554.3 | P1 | |
PARP14 | ENST00000460683.1 | c.904A>G | p.Lys302Glu | missense_variant, NMD_transcript_variant | 3/14 | 5 | |||
PARP14 | ENST00000649945.1 | c.836-3807A>G | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000402 AC: 10AN: 248996Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135116
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461608Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 727084
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | The c.1381A>G (p.K461E) alteration is located in exon 6 (coding exon 6) of the PARP14 gene. This alteration results from a A to G substitution at nucleotide position 1381, causing the lysine (K) at amino acid position 461 to be replaced by a glutamic acid (E). 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