rs727504685
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_032119.4(ADGRV1):c.9590T>C(p.Leu3197Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000689 in 1,452,312 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 Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. L3197L) has been classified as Likely benign.
Frequency
Consequence
NM_032119.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRV1 | NM_032119.4 | c.9590T>C | p.Leu3197Ser | missense_variant | 44/90 | ENST00000405460.9 | |
LOC105379077 | XR_001742802.2 | n.364-4381A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRV1 | ENST00000405460.9 | c.9590T>C | p.Leu3197Ser | missense_variant | 44/90 | 1 | NM_032119.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1452312Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 721824
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 16, 2013 | Variant classified as Uncertain Significance - Favor Benign. The Leu3197Ser vari ant in GPR98 has not been reported in individuals with hearing loss or in large population studies. Computational analyses (biochemical amino acid properties, c onservation, AlignGVGD, PolyPhen2, and SIFT) do not provide strong support for a n impact to the protein. Of note, medaka has a serine (Ser) at this position des pite high nearby amino acid conservation. In summary, additional data is needed to determine the clinical significance of this variant; however based upon the l ack of conservation and computation analyses, we would lean towards a more likel y benign role. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at