rs6138900
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001318207.1(TMEM239):c.*1381G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,370 control chromosomes in the GnomAD database, including 3,368 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.16 ( 3368 hom., cov: 33)
Exomes 𝑓: 0.057 ( 0 hom. )
Consequence
TMEM239
NM_001318207.1 3_prime_UTR
NM_001318207.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.439
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM239 | NM_001318207.1 | c.*1381G>C | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM239 | ENST00000361033.1 | c.*1381G>C | 3_prime_UTR_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.164 AC: 24896AN: 152112Hom.: 3356 Cov.: 33
GnomAD3 genomes
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GnomAD4 exome AF: 0.0571 AC: 8AN: 140Hom.: 0 Cov.: 0 AF XY: 0.0377 AC XY: 4AN XY: 106
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GnomAD4 genome ? AF: 0.164 AC: 24944AN: 152230Hom.: 3368 Cov.: 33 AF XY: 0.162 AC XY: 12051AN XY: 74440
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at