rs9470794
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021943.3(ZFAND3):c.530-13167T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,196 control chromosomes in the GnomAD database, including 1,330 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 0.12 ( 1330 hom., cov: 32)
Consequence
ZFAND3
NM_021943.3 intron
NM_021943.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.39
Genes affected
ZFAND3 (HGNC:18019): (zinc finger AN1-type containing 3) Predicted to enable DNA binding activity and zinc ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]
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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=-1.0).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFAND3 | NM_021943.3 | c.530-13167T>C | intron_variant | ENST00000287218.9 | |||
LOC124901314 | XR_007059570.1 | n.15124T>C | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFAND3 | ENST00000287218.9 | c.530-13167T>C | intron_variant | 1 | NM_021943.3 | P1 | |||
ZFAND3 | ENST00000373389.5 | c.459-3191T>C | intron_variant | 5 | |||||
ZFAND3 | ENST00000373391.6 | c.464-13167T>C | intron_variant | 5 | |||||
ZFAND3 | ENST00000440482.2 | n.212-13167T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.119 AC: 18062AN: 152078Hom.: 1326 Cov.: 32
GnomAD3 genomes
?
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18062
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152078
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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: 0.119 AC: 18081AN: 152196Hom.: 1330 Cov.: 32 AF XY: 0.118 AC XY: 8791AN XY: 74414
GnomAD4 genome
?
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AC:
18081
AN:
152196
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Cov.:
32
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AC XY:
8791
AN XY:
74414
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Asia WGS
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673
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3478
ClinVar
Not reported inComputational scores
Source:
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