rs59693083
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_049793.1(WAKMAR2):n.895-75T>C 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 0.191 in 152,420 control chromosomes in the GnomAD database, including 5,019 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 0.19 ( 5019 hom., cov: 32)
Exomes 𝑓: 0.066 ( 0 hom. )
Consequence
WAKMAR2
NR_049793.1 intron, non_coding_transcript
NR_049793.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.323
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=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WAKMAR2 | NR_049793.1 | n.895-75T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WAKMAR2 | ENST00000606998.1 | n.895-75T>C | intron_variant, non_coding_transcript_variant | 2 | ||||||
WAKMAR2 | ENST00000448942.5 | n.63+2247T>C | intron_variant, non_coding_transcript_variant | 5 | ||||||
WAKMAR2 | ENST00000607671.1 | n.63+2247T>C | intron_variant, non_coding_transcript_variant | 5 | ||||||
WAKMAR2 | ENST00000662141.1 | n.391-23T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.191 AC: 29066AN: 152072Hom.: 4998 Cov.: 32
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GnomAD4 exome AF: 0.0658 AC: 15AN: 228Hom.: 0 AF XY: 0.0429 AC XY: 6AN XY: 140
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GnomAD4 genome AF: 0.191 AC: 29138AN: 152192Hom.: 5019 Cov.: 32 AF XY: 0.185 AC XY: 13802AN XY: 74438
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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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at