11-118957207-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 3P and 8B. PM2PP3BP6_Very_Strong
The NM_006760.4(UPK2):c.209-1G>A variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000145 in 1,614,070 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006760.4 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000821 AC: 125AN: 152166Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000175 AC: 44AN: 251288Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135796
GnomAD4 exome AF: 0.0000746 AC: 109AN: 1461786Hom.: 0 Cov.: 33 AF XY: 0.0000564 AC XY: 41AN XY: 727210
GnomAD4 genome AF: 0.000821 AC: 125AN: 152284Hom.: 0 Cov.: 31 AF XY: 0.000739 AC XY: 55AN 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