chr3-151328800-A-G
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_176894.3(P2RY13):āc.256T>Cā(p.Leu86=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000297 in 1,613,930 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00030 ( 0 hom., cov: 32)
Exomes š: 0.00030 ( 0 hom. )
Consequence
P2RY13
NM_176894.3 synonymous
NM_176894.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.02
Genes affected
P2RY13 (HGNC:4537): (purinergic receptor P2Y13) The product of this gene belongs to the family of G-protein coupled receptors. This family has several receptor subtypes with different pharmacological selectivity, which overlaps in some cases, for various adenosine and uridine nucleotides. This receptor is activated by ADP. [provided by RefSeq, Sep 2008]
MED12L (HGNC:16050): (mediator complex subunit 12L) The protein encoded by this gene is part of the Mediator complex, which is involved in transcriptional coactivation of nearly all RNA polymerase II-dependent genes. The Mediator complex links gene-specific transcriptional activators with the basal transcription machinery. [provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 3-151328800-A-G is Benign according to our data. Variant chr3-151328800-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2654233.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.02 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
P2RY13 | NM_176894.3 | c.256T>C | p.Leu86= | synonymous_variant | 2/2 | ENST00000325602.6 | |
MED12L | NM_001393769.1 | c.2251-21259A>G | intron_variant | ENST00000687756.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P2RY13 | ENST00000325602.6 | c.256T>C | p.Leu86= | synonymous_variant | 2/2 | 1 | NM_176894.3 | P1 | |
MED12L | ENST00000687756.1 | c.2251-21259A>G | intron_variant | NM_001393769.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000296 AC: 45AN: 152090Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000188 AC: 47AN: 250412Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135294
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GnomAD4 exome AF: 0.000298 AC: 435AN: 1461722Hom.: 0 Cov.: 34 AF XY: 0.000285 AC XY: 207AN XY: 727158
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GnomAD4 genome AF: 0.000296 AC: 45AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74430
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | P2RY13: BP4, BP7 - |
Computational scores
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Benign
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DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at