12-15681305-G-GTAATAATAA
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_004447.6(EPS8):c.60-12_60-4dupTTATTATTA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00147 in 1,083,770 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004447.6 splice_region, intron
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: 0.00532 AC: 781AN: 146940Hom.: 3 Cov.: 27
GnomAD3 exomes AF: 0.000942 AC: 144AN: 152932Hom.: 0 AF XY: 0.000877 AC XY: 75AN XY: 85482
GnomAD4 exome AF: 0.000860 AC: 806AN: 936802Hom.: 1 Cov.: 11 AF XY: 0.000854 AC XY: 403AN XY: 471830
GnomAD4 genome AF: 0.00533 AC: 784AN: 146968Hom.: 4 Cov.: 27 AF XY: 0.00574 AC XY: 410AN XY: 71490
ClinVar
Submissions by phenotype
not provided Benign:2
EPS8: BP4, BS1 -
- -
EPS8-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at