chr11-66564100-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_003793.4(CTSF):c.1368C>T(p.Asp456Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00135 in 1,613,684 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003793.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00694 AC: 1057AN: 152238Hom.: 11 Cov.: 33
GnomAD3 exomes AF: 0.00182 AC: 453AN: 248968Hom.: 3 AF XY: 0.00147 AC XY: 198AN XY: 134766
GnomAD4 exome AF: 0.000765 AC: 1118AN: 1461328Hom.: 17 Cov.: 33 AF XY: 0.000671 AC XY: 488AN XY: 726896
GnomAD4 genome AF: 0.00692 AC: 1054AN: 152356Hom.: 11 Cov.: 33 AF XY: 0.00703 AC XY: 524AN XY: 74506
ClinVar
Submissions by phenotype
not provided Benign:4
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Neuronal ceroid lipofuscinosis 13 Benign:3
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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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at