chr16-75464597-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_145254.3(TMEM170A):c.4G>A(p.Glu2Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000126 in 1,584,206 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145254.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM170A | NM_145254.3 | c.4G>A | p.Glu2Lys | missense_variant | 1/3 | ENST00000561878.2 | |
TMEM170A | NM_001304996.2 | c.4G>A | p.Glu2Lys | missense_variant | 1/3 | ||
TMEM170A | NM_001304998.1 | c.-3+75G>A | intron_variant | ||||
TMEM170A | XM_017022941.2 | c.-3+75G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM170A | ENST00000561878.2 | c.4G>A | p.Glu2Lys | missense_variant | 1/3 | 1 | NM_145254.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152266Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.0000133 AC: 19AN: 1431940Hom.: 0 Cov.: 33 AF XY: 0.00000983 AC XY: 7AN XY: 712220
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152266Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74394
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2024 | The c.4G>A (p.E2K) alteration is located in exon 1 (coding exon 1) of the TMEM170A gene. This alteration results from a G to A substitution at nucleotide position 4, causing the glutamic acid (E) at amino acid position 2 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