NM_018487.3:c.73C>A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018487.3(TMEM176A):c.73C>A(p.Gln25Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000093 in 1,613,516 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018487.3 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 |
---|---|---|---|---|---|---|---|---|
TMEM176A | NM_018487.3 | c.73C>A | p.Gln25Lys | missense_variant | Exon 2 of 7 | ENST00000004103.8 | NP_060957.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249232Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135052
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461316Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726982
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.73C>A (p.Q25K) alteration is located in exon 2 (coding exon 1) of the TMEM176A gene. This alteration results from a C to A substitution at nucleotide position 73, causing the glutamine (Q) at amino acid position 25 to be replaced by a lysine (K). 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