19-54163088-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_144686.4(TMC4):c.1349G>A(p.Gly450Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,614,052 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144686.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMC4 | NM_144686.4 | c.1349G>A | p.Gly450Asp | missense_variant | Exon 9 of 15 | ENST00000619895.5 | NP_653287.2 | |
TMC4 | NM_001145303.3 | c.1367G>A | p.Gly456Asp | missense_variant | Exon 9 of 15 | NP_001138775.2 | ||
TMC4 | XM_011526486.3 | c.887G>A | p.Gly296Asp | missense_variant | Exon 6 of 12 | XP_011524788.1 | ||
TMC4 | XR_935741.3 | n.1410G>A | non_coding_transcript_exon_variant | Exon 9 of 15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMC4 | ENST00000619895.5 | c.1349G>A | p.Gly450Asp | missense_variant | Exon 9 of 15 | 1 | NM_144686.4 | ENSP00000479458.1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152046Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251480Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135916
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461888Hom.: 1 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727242
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152164Hom.: 0 Cov.: 31 AF XY: 0.0000538 AC XY: 4AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1367G>A (p.G456D) alteration is located in exon 9 (coding exon 9) of the TMC4 gene. This alteration results from a G to A substitution at nucleotide position 1367, causing the glycine (G) at amino acid position 456 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at