rs576743510
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_032119.4(ADGRV1):c.12148G>A(p.Asp4050Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000128 in 1,593,016 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 (★★). Synonymous variant affecting the same amino acid position (i.e. D4050D) has been classified as Likely benign.
Frequency
Consequence
NM_032119.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRV1 | NM_032119.4 | c.12148G>A | p.Asp4050Asn | missense_variant | 59/90 | ENST00000405460.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRV1 | ENST00000405460.9 | c.12148G>A | p.Asp4050Asn | missense_variant | 59/90 | 1 | NM_032119.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000332 AC: 5AN: 150690Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000374 AC: 92AN: 246200Hom.: 0 AF XY: 0.000262 AC XY: 35AN XY: 133516
GnomAD4 exome AF: 0.000138 AC: 199AN: 1442218Hom.: 0 Cov.: 31 AF XY: 0.000102 AC XY: 73AN XY: 714390
GnomAD4 genome ? AF: 0.0000332 AC: 5AN: 150798Hom.: 0 Cov.: 32 AF XY: 0.0000544 AC XY: 4AN XY: 73552
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 04, 2023 | See Variant Classification Assertion Criteria. - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 11, 2016 | p.Asp4050Asn in exon 50 of GPR98: This variant is not expected to have clinical significance because it has been identified in 0.4% (43/10654) of Latino chromos omes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs576743510). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at