chr1-25811645-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020451.3(SELENON):c.1093-46C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 1,608,850 control chromosomes in the GnomAD database, including 481,014 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_020451.3 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: 0.699 AC: 106247AN: 151984Hom.: 38885 Cov.: 32
GnomAD3 exomes AF: 0.790 AC: 194529AN: 246134Hom.: 78350 AF XY: 0.795 AC XY: 106372AN XY: 133820
GnomAD4 exome AF: 0.776 AC: 1130371AN: 1456748Hom.: 442108 Cov.: 32 AF XY: 0.780 AC XY: 565250AN XY: 724996
GnomAD4 genome AF: 0.699 AC: 106303AN: 152102Hom.: 38906 Cov.: 32 AF XY: 0.705 AC XY: 52430AN XY: 74338
ClinVar
Submissions by phenotype
not provided Benign:2
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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. -
not specified Benign:1
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Eichsfeld type congenital muscular dystrophy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at