12-123697201-G-C
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_024809.5(TCTN2):c.1505+3G>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000722 in 1,600,364 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_024809.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00357 AC: 544AN: 152182Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.000959 AC: 241AN: 251408Hom.: 1 AF XY: 0.000787 AC XY: 107AN XY: 135878
GnomAD4 exome AF: 0.000423 AC: 612AN: 1448064Hom.: 3 Cov.: 27 AF XY: 0.000395 AC XY: 285AN XY: 721486
GnomAD4 genome AF: 0.00357 AC: 544AN: 152300Hom.: 3 Cov.: 33 AF XY: 0.00348 AC XY: 259AN XY: 74466
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
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Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at