NM_032119.4:c.2241-10A>T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_032119.4(ADGRV1):c.2241-10A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00135 in 1,607,876 control chromosomes in the GnomAD database, including 85 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_032119.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADGRV1 | ENST00000405460.9 | c.2241-10A>T | intron_variant | Intron 11 of 89 | 1 | NM_032119.4 | ENSP00000384582.2 | |||
ADGRV1 | ENST00000640403.1 | c.-457-10A>T | intron_variant | Intron 1 of 28 | 5 | ENSP00000492531.1 | ||||
ADGRV1 | ENST00000504142.2 | n.1007-10A>T | intron_variant | Intron 5 of 13 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000901 AC: 137AN: 152078Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00140 AC: 339AN: 242804Hom.: 7 AF XY: 0.00131 AC XY: 172AN XY: 131440
GnomAD4 exome AF: 0.00140 AC: 2032AN: 1455680Hom.: 79 Cov.: 32 AF XY: 0.00136 AC XY: 984AN XY: 723656
GnomAD4 genome AF: 0.000900 AC: 137AN: 152196Hom.: 6 Cov.: 33 AF XY: 0.00108 AC XY: 80AN XY: 74406
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:1
c.2241-10A>T in intron 11 of GPR98: This variant is not expected to have clinica l significance because it does not cause the splice site sequence to diverge fro m consensus. It has been identified in 5.1% (9/178) of Japanese chromosomes and 1.0% (2/194) of Han Chinese chromosomes by the 1000 Genomes Project (dbSNP rs150 996234). -
Usher syndrome type 2C Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Febrile seizures, familial, 4;C2931213:Usher syndrome type 2C Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at