chr13-33016455-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_004795.4(KL):c.15C>T(p.Ala5Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00151 in 964,242 control chromosomes in the GnomAD database, including 3 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_004795.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000912 AC: 131AN: 143650Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0156 AC: 1AN: 64Hom.: 0 AF XY: 0.0263 AC XY: 1AN XY: 38
GnomAD4 exome AF: 0.00162 AC: 1328AN: 820536Hom.: 3 Cov.: 27 AF XY: 0.00169 AC XY: 642AN XY: 380462
GnomAD4 genome AF: 0.000912 AC: 131AN: 143706Hom.: 0 Cov.: 30 AF XY: 0.000616 AC XY: 43AN XY: 69822
ClinVar
Submissions by phenotype
Tumoral calcinosis, hyperphosphatemic, familial, 3 Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at