X-149604010-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_032508.4(TMEM185A):c.484A>G(p.Lys162Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000157 in 1,207,771 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032508.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM185A | NM_032508.4 | c.484A>G | p.Lys162Glu | missense_variant | Exon 4 of 7 | ENST00000600449.8 | NP_115897.1 | |
TMEM185A | NM_001174092.3 | c.307A>G | p.Lys103Glu | missense_variant | Exon 3 of 6 | NP_001167563.1 | ||
TMEM185A | NM_001282302.2 | c.484A>G | p.Lys162Glu | missense_variant | Exon 4 of 4 | NP_001269231.1 | ||
TMEM185A | NR_104121.2 | n.251-3531A>G | intron_variant | Intron 1 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000893 AC: 1AN: 112003Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34149
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 181359Hom.: 0 AF XY: 0.0000152 AC XY: 1AN XY: 65869
GnomAD4 exome AF: 0.0000164 AC: 18AN: 1095768Hom.: 0 Cov.: 28 AF XY: 0.0000221 AC XY: 8AN XY: 361292
GnomAD4 genome AF: 0.00000893 AC: 1AN: 112003Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34149
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.484A>G (p.K162E) alteration is located in exon 4 (coding exon 4) of the TMEM185A gene. This alteration results from a A to G substitution at nucleotide position 484, causing the lysine (K) at amino acid position 162 to be replaced by a glutamic acid (E). 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