chrX-153982595-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003492.3(TMEM187):c.533C>T(p.Ala178Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000297 in 1,210,150 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 15 hemizygotes in GnomAD. 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_003492.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM187 | NM_003492.3 | c.533C>T | p.Ala178Val | missense_variant | 2/2 | ENST00000369982.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM187 | ENST00000369982.5 | c.533C>T | p.Ala178Val | missense_variant | 2/2 | 1 | NM_003492.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000265 AC: 3AN: 113195Hom.: 0 Cov.: 25 AF XY: 0.0000283 AC XY: 1AN XY: 35331
GnomAD3 exomes AF: 0.0000443 AC: 8AN: 180495Hom.: 0 AF XY: 0.000107 AC XY: 7AN XY: 65385
GnomAD4 exome AF: 0.0000301 AC: 33AN: 1096955Hom.: 0 Cov.: 33 AF XY: 0.0000386 AC XY: 14AN XY: 362589
GnomAD4 genome ? AF: 0.0000265 AC: 3AN: 113195Hom.: 0 Cov.: 25 AF XY: 0.0000283 AC XY: 1AN XY: 35331
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 15, 2023 | The c.533C>T (p.A178V) alteration is located in exon 2 (coding exon 1) of the TMEM187 gene. This alteration results from a C to T substitution at nucleotide position 533, causing the alanine (A) at amino acid position 178 to be replaced by a valine (V). 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