rs10450321
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000457388.1(TMEM161BP1):n.517T>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0733 in 1,497,384 control chromosomes in the GnomAD database, including 4,448 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 0.089 ( 753 hom., cov: 32)
Exomes 𝑓: 0.071 ( 3695 hom. )
Consequence
TMEM161BP1
ENST00000457388.1 non_coding_transcript_exon
ENST00000457388.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.55
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=-0.52).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM161BP1 | use as main transcript | n.37337931T>C | intragenic_variant | |||||
LINC00993 | NR_104061.1 | n.314-4395T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM161BP1 | ENST00000457388.1 | n.517T>C | non_coding_transcript_exon_variant | 1/1 | 6 | |||||
ENSG00000290801 | ENST00000426471.6 | n.315-4395T>C | intron_variant | 2 | ||||||
ENSG00000290801 | ENST00000435629.5 | n.204-4395T>C | intron_variant | 3 | ||||||
ENSG00000290801 | ENST00000606476.1 | n.158-4395T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0887 AC: 13497AN: 152096Hom.: 727 Cov.: 32
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GnomAD4 exome AF: 0.0715 AC: 96153AN: 1345170Hom.: 3695 Cov.: 23 AF XY: 0.0708 AC XY: 47894AN XY: 676158
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GnomAD4 genome AF: 0.0892 AC: 13578AN: 152214Hom.: 753 Cov.: 32 AF XY: 0.0878 AC XY: 6534AN XY: 74428
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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