7-75992223-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_031925.3(TMEM120A):c.238G>A(p.Ala80Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000447 in 1,611,354 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_031925.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM120A | NM_031925.3 | c.238G>A | p.Ala80Thr | missense_variant | 3/12 | ENST00000493111.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM120A | ENST00000493111.7 | c.238G>A | p.Ala80Thr | missense_variant | 3/12 | 1 | NM_031925.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000851 AC: 21AN: 246804Hom.: 1 AF XY: 0.000127 AC XY: 17AN XY: 134136
GnomAD4 exome AF: 0.0000487 AC: 71AN: 1459006Hom.: 1 Cov.: 31 AF XY: 0.0000799 AC XY: 58AN XY: 725670
GnomAD4 genome ? AF: 0.00000656 AC: 1AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.238G>A (p.A80T) alteration is located in exon 3 (coding exon 3) of the TMEM120A gene. This alteration results from a G to A substitution at nucleotide position 238, causing the alanine (A) at amino acid position 80 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