11-130903384-C-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The NM_014758.3(SNX19):āc.2444G>Cā(p.Gly815Ala) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00866 in 1,611,990 control chromosomes in the GnomAD database, including 89 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/25 in silico tools predict a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_014758.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00688 AC: 1047AN: 152132Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00688 AC: 1724AN: 250642Hom.: 15 AF XY: 0.00671 AC XY: 909AN XY: 135454
GnomAD4 exome AF: 0.00884 AC: 12907AN: 1459740Hom.: 80 Cov.: 31 AF XY: 0.00866 AC XY: 6288AN XY: 726214
GnomAD4 genome AF: 0.00688 AC: 1047AN: 152250Hom.: 9 Cov.: 32 AF XY: 0.00615 AC XY: 458AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at