chr5-90776582-G-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS1
The NM_032119.4(ADGRV1):c.12527+6G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000344 in 1,613,048 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_032119.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00176 AC: 268AN: 152034Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000450 AC: 112AN: 248946Hom.: 0 AF XY: 0.000392 AC XY: 53AN XY: 135062
GnomAD4 exome AF: 0.000194 AC: 284AN: 1460898Hom.: 1 Cov.: 31 AF XY: 0.000197 AC XY: 143AN XY: 726752
GnomAD4 genome AF: 0.00178 AC: 271AN: 152150Hom.: 1 Cov.: 32 AF XY: 0.00179 AC XY: 133AN XY: 74370
ClinVar
Submissions by phenotype
not provided Benign:5
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not specified Uncertain:1Benign:3
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12527+6G>T in Intron 61 of GPR98: This variant is not expected to have clinical significance because it has been identified in 0.6% (17/3032) of African America n chromosomes from a broad population by the NHLBI Exome Sequencing Project (htt p://evs.gs.washington.edu/EVS; dbSNP rs141701016). -
Usher syndrome type 2C Benign:1
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ADGRV1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at