rs1521882
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001277372.4(KIAA2012):c.370-5642G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,194 control chromosomes in the GnomAD database, including 51,531 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 0.82 ( 51531 hom., cov: 33)
Consequence
KIAA2012
NM_001277372.4 intron
NM_001277372.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.682
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=-0.98).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA2012 | NM_001277372.4 | c.370-5642G>A | intron_variant | ENST00000498697.3 | |||
KIAA2012 | NM_001367720.2 | c.370-5642G>A | intron_variant | ||||
KIAA2012 | XM_017003112.3 | c.370-5642G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA2012 | ENST00000498697.3 | c.370-5642G>A | intron_variant | 5 | NM_001277372.4 | P1 | |||
KIAA2012-AS1 | ENST00000409819.2 | n.3214-9562C>T | intron_variant, non_coding_transcript_variant | 2 | |||||
KIAA2012 | ENST00000459709.5 | c.538-5642G>A | intron_variant | 2 | |||||
KIAA2012 | ENST00000409515.3 | n.709-5642G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.821 AC: 124841AN: 152076Hom.: 51474 Cov.: 33
GnomAD3 genomes
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152076
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.821 AC: 124960AN: 152194Hom.: 51531 Cov.: 33 AF XY: 0.822 AC XY: 61157AN XY: 74406
GnomAD4 genome
?
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124960
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152194
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33
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61157
AN XY:
74406
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2353
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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
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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