rs143140501
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_001127198.5(TMC6):c.2021+11C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.028 in 1,602,370 control chromosomes in the GnomAD database, including 695 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001127198.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMC6 | NM_001127198.5 | c.2021+11C>T | intron_variant | Intron 16 of 19 | ENST00000590602.6 | NP_001120670.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0247 AC: 3744AN: 151786Hom.: 58 Cov.: 33
GnomAD3 exomes AF: 0.0228 AC: 5227AN: 229718Hom.: 62 AF XY: 0.0233 AC XY: 2909AN XY: 124858
GnomAD4 exome AF: 0.0284 AC: 41172AN: 1450464Hom.: 637 Cov.: 32 AF XY: 0.0280 AC XY: 20171AN XY: 720608
GnomAD4 genome AF: 0.0246 AC: 3739AN: 151906Hom.: 58 Cov.: 33 AF XY: 0.0244 AC XY: 1815AN XY: 74254
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
Epidermodysplasia verruciformis Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at