rs17173637
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XR_928171.3(LOC105375567):n.179-3453A>G 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 0.0801 in 152,296 control chromosomes in the GnomAD database, including 565 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 0.080 ( 565 hom., cov: 32)
Consequence
LOC105375567
XR_928171.3 intron, non_coding_transcript
XR_928171.3 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.25
Genes affected
AOC1 (HGNC:80): (amine oxidase copper containing 1) This gene encodes a metal-binding membrane glycoprotein that oxidatively deaminates putrescine, histamine, and related compounds. The encoded protein is inhibited by amiloride, a diuretic that acts by closing epithelial sodium ion channels. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2013]
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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=-0.94).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0897 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC124901775 | XR_007060591.1 | n.258-610T>C | intron_variant, non_coding_transcript_variant | ||||
LOC105375567 | XR_928171.3 | n.179-3453A>G | intron_variant, non_coding_transcript_variant | ||||
LOC105375567 | XR_928169.3 | n.179-3453A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AOC1 | ENST00000467291.5 | c.-93+4959T>C | intron_variant | 5 | P2 | ||||
AOC1 | ENST00000493429.5 | c.-93+4959T>C | intron_variant | 5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0801 AC: 12190AN: 152178Hom.: 564 Cov.: 32
GnomAD3 genomes
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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: 0.0801 AC: 12199AN: 152296Hom.: 565 Cov.: 32 AF XY: 0.0815 AC XY: 6066AN XY: 74474
GnomAD4 genome
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152296
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32
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6066
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74474
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242
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at