X-153982226-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_003492.3(TMEM187):c.164C>T(p.Pro55Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000157 in 1,211,494 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P55P) has been classified as Likely benign.
Frequency
Consequence
NM_003492.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM187 | ENST00000369982.5 | c.164C>T | p.Pro55Leu | missense_variant | Exon 2 of 2 | 1 | NM_003492.3 | ENSP00000358999.4 | ||
TMEM187 | ENST00000425274.1 | c.164C>T | p.Pro55Leu | missense_variant | Exon 2 of 2 | 5 | ENSP00000390108.1 | |||
TMEM187 | ENST00000431598.1 | c.*65C>T | downstream_gene_variant | 3 | ENSP00000412872.1 |
Frequencies
GnomAD3 genomes AF: 0.0000176 AC: 2AN: 113506Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 35652
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 181405Hom.: 0 AF XY: 0.0000150 AC XY: 1AN XY: 66615
GnomAD4 exome AF: 0.0000155 AC: 17AN: 1097988Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 4AN XY: 363480
GnomAD4 genome AF: 0.0000176 AC: 2AN: 113506Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 35652
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.164C>T (p.P55L) 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 164, causing the proline (P) at amino acid position 55 to be replaced by a leucine (L). 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