chr6-37218985-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001286401.2(TMEM217):c.46G>A(p.Val16Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,614,054 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_001286401.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM217 | ENST00000651039.2 | c.46G>A | p.Val16Met | missense_variant | Exon 2 of 3 | NM_001286401.2 | ENSP00000499204.1 | |||
TMEM217B | ENST00000497775.2 | c.-27-5989G>A | intron_variant | Intron 1 of 1 | 2 | NM_001395378.1 | ENSP00000499172.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152196Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000996 AC: 25AN: 250982Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135740
GnomAD4 exome AF: 0.0000410 AC: 60AN: 1461858Hom.: 0 Cov.: 31 AF XY: 0.0000591 AC XY: 43AN XY: 727224
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152196Hom.: 0 Cov.: 31 AF XY: 0.0000807 AC XY: 6AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.46G>A (p.V16M) alteration is located in exon 2 (coding exon 1) of the TMEM217 gene. This alteration results from a G to A substitution at nucleotide position 46, causing the valine (V) at amino acid position 16 to be replaced by a methionine (M). 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