X-129752356-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003399.6(XPNPEP2):c.1017+11C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000646 in 1,205,817 control chromosomes in the GnomAD database, including 3 homozygotes. There are 226 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003399.6 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00317 AC: 355AN: 111874Hom.: 0 Cov.: 23 AF XY: 0.00311 AC XY: 106AN XY: 34056
GnomAD3 exomes AF: 0.000940 AC: 167AN: 177616Hom.: 0 AF XY: 0.000697 AC XY: 44AN XY: 63102
GnomAD4 exome AF: 0.000387 AC: 423AN: 1093890Hom.: 3 Cov.: 31 AF XY: 0.000331 AC XY: 119AN XY: 359598
GnomAD4 genome AF: 0.00318 AC: 356AN: 111927Hom.: 0 Cov.: 23 AF XY: 0.00314 AC XY: 107AN XY: 34119
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at