chr12-123688008-A-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_024809.5(TCTN2):c.765-43A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 1,608,040 control chromosomes in the GnomAD database, including 129,642 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_024809.5 intron
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: 0.414 AC: 62812AN: 151834Hom.: 13855 Cov.: 31
GnomAD3 exomes AF: 0.348 AC: 87439AN: 251046Hom.: 16807 AF XY: 0.353 AC XY: 47994AN XY: 135774
GnomAD4 exome AF: 0.391 AC: 569068AN: 1456090Hom.: 115770 Cov.: 32 AF XY: 0.390 AC XY: 282606AN XY: 724468
GnomAD4 genome AF: 0.414 AC: 62868AN: 151950Hom.: 13872 Cov.: 31 AF XY: 0.408 AC XY: 30274AN XY: 74272
ClinVar
Submissions by phenotype
not specified Benign:2
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Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
not provided Benign:2
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. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at