rs9389316
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_152842.1(AHI1-DT):n.534+7436C>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 0.116 in 151,668 control chromosomes in the GnomAD database, including 2,287 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 0.12 ( 2287 hom., cov: 30)
Consequence
AHI1-DT
NR_152842.1 intron, non_coding_transcript
NR_152842.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.904
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=-0.92).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AHI1-DT | NR_152842.1 | n.534+7436C>A | intron_variant, non_coding_transcript_variant | ||||
AHI1-DT | NR_026805.1 | n.420+7436C>A | intron_variant, non_coding_transcript_variant | ||||
AHI1-DT | NR_152844.1 | n.534+7436C>A | intron_variant, non_coding_transcript_variant | ||||
AHI1-DT | NR_152845.1 | n.658+7436C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AHI1-DT | ENST00000702072.1 | n.367+7436C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.115 AC: 17499AN: 151556Hom.: 2279 Cov.: 30
GnomAD3 genomes
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17499
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30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.116 AC: 17547AN: 151668Hom.: 2287 Cov.: 30 AF XY: 0.112 AC XY: 8327AN XY: 74098
GnomAD4 genome
?
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17547
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30
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8327
AN XY:
74098
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Asia WGS
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362
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3478
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