5-90755167-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_032119.4(ADGRV1):c.11562C>T(p.Ala3854=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000167 in 1,600,996 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A3854A) has been classified as Likely benign.
Frequency
Consequence
NM_032119.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRV1 | NM_032119.4 | c.11562C>T | p.Ala3854= | synonymous_variant | 55/90 | ENST00000405460.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRV1 | ENST00000405460.9 | c.11562C>T | p.Ala3854= | synonymous_variant | 55/90 | 1 | NM_032119.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000322 AC: 49AN: 151952Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000197 AC: 47AN: 238528Hom.: 0 AF XY: 0.000208 AC XY: 27AN XY: 130078
GnomAD4 exome AF: 0.000150 AC: 218AN: 1448926Hom.: 1 Cov.: 30 AF XY: 0.000153 AC XY: 110AN XY: 720720
GnomAD4 genome AF: 0.000322 AC: 49AN: 152070Hom.: 0 Cov.: 32 AF XY: 0.000538 AC XY: 40AN XY: 74342
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 30, 2012 | Ala3854Ala in Exon 55 of GPR98: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 1/2990 African Ameri can chromosomes from a broad population by the NHLBI Exome Sequencing Project (h ttp://evs.gs.washington.edu/EVS). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at