9-68540582-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153237.2(TMEM252):c.233G>A(p.Arg78Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000384 in 1,614,178 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153237.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM252 | NM_153237.2 | c.233G>A | p.Arg78Gln | missense_variant | 1/2 | ENST00000377311.4 | NP_694969.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM252 | ENST00000377311.4 | c.233G>A | p.Arg78Gln | missense_variant | 1/2 | 1 | NM_153237.2 | ENSP00000366528.4 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000797 AC: 20AN: 250976Hom.: 0 AF XY: 0.0000885 AC XY: 12AN XY: 135626
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461850Hom.: 1 Cov.: 31 AF XY: 0.0000413 AC XY: 30AN XY: 727226
GnomAD4 genome AF: 0.0000656 AC: 10AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2023 | The c.233G>A (p.R78Q) alteration is located in exon 1 (coding exon 1) of the TMEM252 gene. This alteration results from a G to A substitution at nucleotide position 233, causing the arginine (R) at amino acid position 78 to be replaced by a glutamine (Q). 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