chr3-129670520-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001017395.5(TMCC1):c.1321G>A(p.Ala441Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,614,204 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001017395.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMCC1 | NM_001017395.5 | c.1321G>A | p.Ala441Thr | missense_variant | 5/7 | ENST00000393238.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMCC1 | ENST00000393238.8 | c.1321G>A | p.Ala441Thr | missense_variant | 5/7 | 1 | NM_001017395.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251278Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135798
GnomAD4 exome AF: 0.000120 AC: 175AN: 1461880Hom.: 0 Cov.: 31 AF XY: 0.000114 AC XY: 83AN XY: 727240
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.1321G>A (p.A441T) alteration is located in exon 4 (coding exon 2) of the TMCC1 gene. This alteration results from a G to A substitution at nucleotide position 1321, causing the alanine (A) at amino acid position 441 to be replaced by a threonine (T). 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