3-151214298-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014879.4(P2RY14):c.19A>C(p.Thr7Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000044 in 1,613,346 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014879.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
P2RY14 | NM_014879.4 | c.19A>C | p.Thr7Pro | missense_variant | 3/3 | ENST00000309170.8 | |
MED12L | NM_001393769.1 | c.2250+20632T>G | intron_variant | ENST00000687756.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P2RY14 | ENST00000309170.8 | c.19A>C | p.Thr7Pro | missense_variant | 3/3 | 1 | NM_014879.4 | P1 | |
MED12L | ENST00000687756.1 | c.2250+20632T>G | intron_variant | NM_001393769.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000522 AC: 13AN: 249104Hom.: 0 AF XY: 0.0000446 AC XY: 6AN XY: 134518
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461168Hom.: 1 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 726838
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.000229 AC XY: 17AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2022 | The c.19A>C (p.T7P) alteration is located in exon 3 (coding exon 1) of the P2RY14 gene. This alteration results from a A to C substitution at nucleotide position 19, causing the threonine (T) at amino acid position 7 to be replaced by a proline (P). 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