21-43776216-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_000100.4(CSTB):c.54C>T(p.His18His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,533,076 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_000100.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000644 AC: 98AN: 152132Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000116 AC: 15AN: 129302Hom.: 0 AF XY: 0.0000851 AC XY: 6AN XY: 70536
GnomAD4 exome AF: 0.0000492 AC: 68AN: 1380834Hom.: 0 Cov.: 31 AF XY: 0.0000337 AC XY: 23AN XY: 681558
GnomAD4 genome AF: 0.000644 AC: 98AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.000618 AC XY: 46AN XY: 74430
ClinVar
Submissions by phenotype
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. -
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. -
Progressive myoclonic epilepsy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at