3-122699802-T-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_017554.3(PARP14):c.1248T>G(p.Asp416Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,846 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.1248T>G | p.Asp416Glu | missense_variant | 6/17 | ENST00000474629.7 | |
PARP14 | XM_011512929.3 | c.1248T>G | p.Asp416Glu | missense_variant | 6/10 | ||
PARP14 | XR_007095695.1 | n.1293T>G | non_coding_transcript_exon_variant | 6/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PARP14 | ENST00000474629.7 | c.1248T>G | p.Asp416Glu | missense_variant | 6/17 | 1 | NM_017554.3 | P1 | |
PARP14 | ENST00000460683.1 | c.771T>G | p.Asp257Glu | missense_variant, NMD_transcript_variant | 3/14 | 5 | |||
PARP14 | ENST00000649945.1 | c.836-3940T>G | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152158Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 248694Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134948
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461688Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727132
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152158Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 28, 2022 | The c.1248T>G (p.D416E) alteration is located in exon 6 (coding exon 6) of the PARP14 gene. This alteration results from a T to G substitution at nucleotide position 1248, causing the aspartic acid (D) at amino acid position 416 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