X-130656575-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006375.4(ENOX2):c.1129+6G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 1,032,789 control chromosomes in the GnomAD database, including 72 homozygotes. There are 3,574 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_006375.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00874 AC: 982AN: 112356Hom.: 4 Cov.: 24 AF XY: 0.00724 AC XY: 250AN XY: 34520
GnomAD3 exomes AF: 0.00840 AC: 1427AN: 169902Hom.: 2 AF XY: 0.00855 AC XY: 492AN XY: 57548
GnomAD4 exome AF: 0.0129 AC: 11875AN: 920381Hom.: 68 Cov.: 16 AF XY: 0.0125 AC XY: 3325AN XY: 265109
GnomAD4 genome AF: 0.00872 AC: 980AN: 112408Hom.: 4 Cov.: 24 AF XY: 0.00720 AC XY: 249AN XY: 34582
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