chr12-82896113-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_152588.3(TMTC2):c.950A>C(p.Tyr317Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,613,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y317C) has been classified as Uncertain significance.
Frequency
Consequence
NM_152588.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMTC2 | NM_152588.3 | c.950A>C | p.Tyr317Ser | missense_variant | 3/12 | ENST00000321196.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMTC2 | ENST00000321196.8 | c.950A>C | p.Tyr317Ser | missense_variant | 3/12 | 1 | NM_152588.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 151988Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000155 AC: 39AN: 251470Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135910
GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727244
GnomAD4 genome ? AF: 0.0000658 AC: 10AN: 151988Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74218
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 23, 2022 | The c.950A>C (p.Y317S) alteration is located in exon 3 (coding exon 3) of the TMTC2 gene. This alteration results from a A to C substitution at nucleotide position 950, causing the tyrosine (Y) at amino acid position 317 to be replaced by a serine (S). 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