rs4916908
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000514065.1(ENSG00000250306):n.288T>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.567 in 153,178 control chromosomes in the GnomAD database, including 26,295 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 0.57 ( 26101 hom., cov: 31)
Exomes 𝑓: 0.54 ( 194 hom. )
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.63
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=-0.65).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM161B-DT | NR_039993.1 | n.207-26838T>C | intron_variant, non_coding_transcript_variant | ||||
TMEM161B-DT | NR_039994.2 | n.165-26838T>C | intron_variant, non_coding_transcript_variant | ||||
TMEM161B-DT | NR_039995.1 | n.207-53038T>C | intron_variant, non_coding_transcript_variant | ||||
TMEM161B-DT | NR_105019.1 | n.586-26838T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000514065.1 | n.288T>C | non_coding_transcript_exon_variant | 1/1 | ||||||
TMEM161B-DT | ENST00000658478.2 | n.206-26838T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.566 AC: 86008AN: 151836Hom.: 26046 Cov.: 31
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GnomAD4 exome AF: 0.536 AC: 656AN: 1224Hom.: 194 Cov.: 0 AF XY: 0.527 AC XY: 390AN XY: 740
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GnomAD4 genome ? AF: 0.567 AC: 86122AN: 151954Hom.: 26101 Cov.: 31 AF XY: 0.565 AC XY: 41970AN XY: 74254
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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