rs41275900
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001130438.3(SPTAN1):c.5478+12G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00138 in 1,613,634 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001130438.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000710 AC: 108AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000607 AC: 152AN: 250248Hom.: 0 AF XY: 0.000584 AC XY: 79AN XY: 135360
GnomAD4 exome AF: 0.00145 AC: 2126AN: 1461308Hom.: 2 Cov.: 38 AF XY: 0.00139 AC XY: 1009AN XY: 726902
GnomAD4 genome AF: 0.000709 AC: 108AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.000685 AC XY: 51AN XY: 74496
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 5 Uncertain:1Benign:2
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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. -
Early infantile epileptic encephalopathy with suppression bursts Benign:1
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not provided Benign:1
SPTAN1: BS1 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at