20-2816844-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001167670.3(TMEM239):c.290C>T(p.Ala97Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000073 in 1,548,828 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001167670.3 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 |
---|---|---|---|---|---|---|---|
TMEM239 | NM_001167670.3 | c.290C>T | p.Ala97Val | missense_variant | 2/2 | ENST00000380585.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM239 | ENST00000380585.2 | c.290C>T | p.Ala97Val | missense_variant | 2/2 | 1 | NM_001167670.3 | P1 | |
TMEM239 | ENST00000361033.1 | c.419C>T | p.Ala140Val | missense_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000199 AC: 30AN: 150710Hom.: 1 AF XY: 0.000262 AC XY: 21AN XY: 80280
GnomAD4 exome AF: 0.0000766 AC: 107AN: 1396502Hom.: 1 Cov.: 36 AF XY: 0.000103 AC XY: 71AN XY: 688914
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152326Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2023 | The c.290C>T (p.A97V) alteration is located in exon 2 (coding exon 1) of the TMEM239 gene. This alteration results from a C to T substitution at nucleotide position 290, causing the alanine (A) at amino acid position 97 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