rs17768650
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_174890.4(ZFAND4):c.328+334C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.032 in 480,870 control chromosomes in the GnomAD database, including 296 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 0.034 ( 97 hom., cov: 32)
Exomes 𝑓: 0.031 ( 199 hom. )
Consequence
ZFAND4
NM_174890.4 intron
NM_174890.4 intron
Scores
2
Splicing: ADA: 0.00001992
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.218
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=-0.89).
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0337 (5132/152224) while in subpopulation EAS AF= 0.0524 (271/5174). AF 95% confidence interval is 0.0473. There are 97 homozygotes in gnomad4. There are 2513 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 97 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFAND4 | NM_174890.4 | c.328+334C>G | intron_variant | ENST00000344646.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFAND4 | ENST00000344646.10 | c.328+334C>G | intron_variant | 1 | NM_174890.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0337 AC: 5123AN: 152106Hom.: 94 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0299 AC: 4457AN: 148998Hom.: 86 AF XY: 0.0300 AC XY: 2410AN XY: 80276
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GnomAD4 exome AF: 0.0313 AC: 10275AN: 328646Hom.: 199 Cov.: 0 AF XY: 0.0302 AC XY: 5591AN XY: 185028
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GnomAD4 genome ? AF: 0.0337 AC: 5132AN: 152224Hom.: 97 Cov.: 32 AF XY: 0.0338 AC XY: 2513AN XY: 74440
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at