chr16-8796586-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015421.4(TMEM186):c.8C>T(p.Ala3Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000168 in 1,611,538 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015421.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM186 | NM_015421.4 | c.8C>T | p.Ala3Val | missense_variant | 2/2 | ENST00000333050.7 | |
LOC124903642 | XR_007064978.1 | n.2468G>A | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM186 | ENST00000333050.7 | c.8C>T | p.Ala3Val | missense_variant | 2/2 | 1 | NM_015421.4 | P1 | |
PMM2 | ENST00000566983.5 | c.-15-5213G>A | intron_variant | 5 | |||||
TMEM186 | ENST00000564869.1 | n.31+1026C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000160 AC: 40AN: 249680Hom.: 0 AF XY: 0.000141 AC XY: 19AN XY: 135036
GnomAD4 exome AF: 0.000161 AC: 235AN: 1459236Hom.: 0 Cov.: 31 AF XY: 0.000160 AC XY: 116AN XY: 725774
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152302Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2023 | The c.8C>T (p.A3V) alteration is located in exon 2 (coding exon 2) of the TMEM186 gene. This alteration results from a C to T substitution at nucleotide position 8, causing the alanine (A) at amino acid position 3 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