11-130903346-G-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_014758.3(SNX19):āc.2482C>Gā(p.Leu828Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00451 in 1,613,236 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_014758.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00283 AC: 430AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00278 AC: 698AN: 251260Hom.: 5 AF XY: 0.00273 AC XY: 371AN XY: 135796
GnomAD4 exome AF: 0.00469 AC: 6845AN: 1460950Hom.: 21 Cov.: 31 AF XY: 0.00451 AC XY: 3281AN XY: 726818
GnomAD4 genome AF: 0.00282 AC: 430AN: 152286Hom.: 0 Cov.: 32 AF XY: 0.00247 AC XY: 184AN XY: 74464
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