chr9-5762533-A-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020829.4(RIC1):c.1993-8A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 1,610,362 control chromosomes in the GnomAD database, including 117,467 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 Benign (★★).
Frequency
Consequence
NM_020829.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.343 AC: 52106AN: 151882Hom.: 9623 Cov.: 32
GnomAD3 exomes AF: 0.404 AC: 100509AN: 248546Hom.: 21273 AF XY: 0.408 AC XY: 54809AN XY: 134198
GnomAD4 exome AF: 0.380 AC: 554104AN: 1458362Hom.: 107831 Cov.: 34 AF XY: 0.383 AC XY: 278050AN XY: 725364
GnomAD4 genome AF: 0.343 AC: 52163AN: 152000Hom.: 9636 Cov.: 32 AF XY: 0.348 AC XY: 25877AN XY: 74294
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Catifa syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at