rs10513650
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000494118.5(ZNF385D):c.389+45524A>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.057 in 152,304 control chromosomes in the GnomAD database, including 582 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 0.057 ( 582 hom., cov: 33)
Consequence
ZNF385D
ENST00000494118.5 intron, NMD_transcript
ENST00000494118.5 intron, NMD_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.583
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 (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF385D | XM_011534122.3 | c.326-139104A>G | intron_variant | ||||
ZNF385D | XM_011534123.3 | c.326-139104A>G | intron_variant | ||||
ZNF385D | XM_011534124.4 | c.326-139104A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF385D | ENST00000494118.5 | c.389+45524A>G | intron_variant, NMD_transcript_variant | 1 | |||||
ZNF385D | ENST00000494108.3 | c.326-139104A>G | intron_variant | 5 | P2 | ||||
ZNF385D | ENST00000706131.1 | c.326-139104A>G | intron_variant | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0571 AC: 8684AN: 152184Hom.: 578 Cov.: 33
GnomAD3 genomes
?
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8684
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152184
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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: 0.0570 AC: 8688AN: 152304Hom.: 582 Cov.: 33 AF XY: 0.0628 AC XY: 4679AN XY: 74472
GnomAD4 genome
?
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AC:
8688
AN:
152304
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Cov.:
33
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4679
AN XY:
74472
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Asia WGS
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635
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3476
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