rs201411901
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001130438.3(SPTAN1):c.6190G>A(p.Ala2064Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000147 in 1,614,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001130438.3 missense
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: 0.0000920 AC: 14AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000541 AC: 136AN: 251456Hom.: 0 AF XY: 0.000412 AC XY: 56AN XY: 135910
GnomAD4 exome AF: 0.000153 AC: 223AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.000116 AC XY: 84AN XY: 727248
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74464
ClinVar
Submissions by phenotype
not specified Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Early infantile epileptic encephalopathy with suppression bursts Benign:1
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not provided Benign:1
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Developmental and epileptic encephalopathy, 5 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at