2-117887500-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000430851.1(HTR5BP):n.819-15503G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0882 in 152,180 control chromosomes in the GnomAD database, including 667 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 0.088 ( 667 hom., cov: 32)
Consequence
HTR5BP
ENST00000430851.1 intron, non_coding_transcript
ENST00000430851.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.00900
Genes affected
HTR5BP (HGNC:16291): (5-hydroxytryptamine receptor 5B, pseudogene)
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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=-0.92).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR5BP | ENST00000430851.1 | n.819-15503G>A | intron_variant, non_coding_transcript_variant | ||||||
ENST00000434708.1 | n.114-15503G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0880 AC: 13380AN: 152062Hom.: 660 Cov.: 32
GnomAD3 genomes
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13380
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0882 AC: 13425AN: 152180Hom.: 667 Cov.: 32 AF XY: 0.0922 AC XY: 6856AN XY: 74394
GnomAD4 genome
?
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AC:
13425
AN:
152180
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Cov.:
32
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6856
AN XY:
74394
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Asia WGS
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255
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at