chr3-151214145-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_014879.4(P2RY14):āc.172A>Gā(p.Ile58Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,613,994 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 Likely benign (ā ).
Frequency
Consequence
NM_014879.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
P2RY14 | NM_014879.4 | c.172A>G | p.Ile58Val | missense_variant | 3/3 | ENST00000309170.8 | NP_055694.3 | |
MED12L | NM_001393769.1 | c.2250+20479T>C | intron_variant | ENST00000687756.1 | NP_001380698.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
P2RY14 | ENST00000309170.8 | c.172A>G | p.Ile58Val | missense_variant | 3/3 | 1 | NM_014879.4 | ENSP00000308361 | P1 | |
MED12L | ENST00000687756.1 | c.2250+20479T>C | intron_variant | NM_001393769.1 | ENSP00000508695 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 251148Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135706
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461838Hom.: 0 Cov.: 32 AF XY: 0.0000426 AC XY: 31AN XY: 727226
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74330
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 17, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at