chrX-153982610-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_003492.3(TMEM187):c.548G>A(p.Arg183Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000256 in 1,210,931 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 12 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM187 | NM_003492.3 | c.548G>A | p.Arg183Lys | missense_variant | 2/2 | ENST00000369982.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM187 | ENST00000369982.5 | c.548G>A | p.Arg183Lys | missense_variant | 2/2 | 1 | NM_003492.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000883 AC: 10AN: 113280Hom.: 0 Cov.: 24 AF XY: 0.000113 AC XY: 4AN XY: 35412
GnomAD3 exomes AF: 0.0000165 AC: 3AN: 181800Hom.: 0 AF XY: 0.0000150 AC XY: 1AN XY: 66478
GnomAD4 exome AF: 0.0000191 AC: 21AN: 1097651Hom.: 0 Cov.: 33 AF XY: 0.0000220 AC XY: 8AN XY: 363117
GnomAD4 genome ? AF: 0.0000883 AC: 10AN: 113280Hom.: 0 Cov.: 24 AF XY: 0.000113 AC XY: 4AN XY: 35412
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.548G>A (p.R183K) alteration is located in exon 2 (coding exon 1) of the TMEM187 gene. This alteration results from a G to A substitution at nucleotide position 548, causing the arginine (R) at amino acid position 183 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