rs17145612
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_019046.3(ANKRD16):c.*33+1628C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0218 in 152,290 control chromosomes in the GnomAD database, including 90 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 0.022 ( 90 hom., cov: 33)
Consequence
ANKRD16
NM_019046.3 intron
NM_019046.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.601
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=-0.91).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0958 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKRD16 | NM_019046.3 | c.*33+1628C>T | intron_variant | ENST00000380094.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKRD16 | ENST00000380094.10 | c.*33+1628C>T | intron_variant | 2 | NM_019046.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0218 AC: 3312AN: 152172Hom.: 90 Cov.: 33
GnomAD3 genomes
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3312
AN:
152172
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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: 0.0218 AC: 3313AN: 152290Hom.: 90 Cov.: 33 AF XY: 0.0230 AC XY: 1716AN XY: 74466
GnomAD4 genome
?
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AC:
3313
AN:
152290
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Cov.:
33
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AC XY:
1716
AN XY:
74466
Gnomad4 AFR
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Asia WGS
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AC:
243
AN:
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