chr5-90653390-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_032119.4(ADGRV1):c.3816G>A(p.Leu1272Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,934 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 (★★).
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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADGRV1 | ENST00000405460.9 | c.3816G>A | p.Leu1272Leu | synonymous_variant | Exon 20 of 90 | 1 | NM_032119.4 | ENSP00000384582.2 | ||
ADGRV1 | ENST00000640403.1 | c.1107G>A | p.Leu369Leu | synonymous_variant | Exon 10 of 29 | 5 | ENSP00000492531.1 | |||
ADGRV1 | ENST00000504142.2 | n.2582G>A | non_coding_transcript_exon_variant | Exon 14 of 14 | 5 | |||||
ADGRV1 | ENST00000639676.1 | n.1414G>A | non_coding_transcript_exon_variant | Exon 8 of 11 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 249094Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135124
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461666Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727112
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74446
ClinVar
Submissions by phenotype
not specified Benign:2
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p.Leu1272Leu in exon 20 of GPR98: This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located within the splice consensus sequence. It has been identified in 2/11478 of Latin o chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstit ute.org; dbSNP rs202004141). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at