12-12717002-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The XM_011520623.4(GPR19):c.-1496G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 996,668 control chromosomes in the GnomAD database, including 93,107 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
XM_011520623.4 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPR19 | XM_011520623.4 | c.-1496G>T | 5_prime_UTR_variant | Exon 1 of 4 | XP_011518925.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.387 AC: 58806AN: 152010Hom.: 12127 Cov.: 33
GnomAD4 exome AF: 0.437 AC: 368860AN: 844544Hom.: 80979 Cov.: 31 AF XY: 0.436 AC XY: 170019AN XY: 390116
GnomAD4 genome AF: 0.387 AC: 58815AN: 152124Hom.: 12128 Cov.: 33 AF XY: 0.390 AC XY: 28992AN XY: 74386
ClinVar
Submissions by phenotype
Multiple endocrine neoplasia type 4 Benign:1
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not provided Benign:1
This variant is associated with the following publications: (PMID: 15061869, 19667240) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at