NM_001127198.5:c.1536-4G>A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001127198.5(TMC6):c.1536-4G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00412 in 1,611,704 control chromosomes in the GnomAD database, including 17 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_001127198.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMC6 | NM_001127198.5 | c.1536-4G>A | splice_region_variant, intron_variant | Intron 12 of 19 | ENST00000590602.6 | NP_001120670.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00270 AC: 410AN: 152124Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00333 AC: 830AN: 249246Hom.: 0 AF XY: 0.00346 AC XY: 467AN XY: 135016
GnomAD4 exome AF: 0.00427 AC: 6232AN: 1459462Hom.: 15 Cov.: 32 AF XY: 0.00420 AC XY: 3045AN XY: 725706
GnomAD4 genome AF: 0.00269 AC: 410AN: 152242Hom.: 2 Cov.: 32 AF XY: 0.00255 AC XY: 190AN XY: 74434
ClinVar
Submissions by phenotype
not provided Benign:4
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TMC6: BP4, BS2 -
Epidermodysplasia verruciformis Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at