rs13149511
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_024936.3(ZCCHC4):c.1011+4798G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.907 in 152,046 control chromosomes in the GnomAD database, including 62,709 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 0.91 ( 62709 hom., cov: 30)
Consequence
ZCCHC4
NM_024936.3 intron
NM_024936.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.75
Genes affected
ZCCHC4 (HGNC:22917): (zinc finger CCHC-type containing 4) Enables S-adenosyl-L-methionine binding activity; rRNA (adenine-N6-)-methyltransferase activity; and zinc ion binding activity. Involved in positive regulation of translation and rRNA methylation. Located in cytoplasm and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZCCHC4 | NM_024936.3 | c.1011+4798G>A | intron_variant | ENST00000302874.9 | |||
ZCCHC4 | XM_011513835.3 | c.1056+3312G>A | intron_variant | ||||
ZCCHC4 | XM_017008129.3 | c.760-5372G>A | intron_variant | ||||
ZCCHC4 | XR_925324.4 | n.1092+3312G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZCCHC4 | ENST00000302874.9 | c.1011+4798G>A | intron_variant | 1 | NM_024936.3 | P1 | |||
ZCCHC4 | ENST00000507760.5 | c.687-5372G>A | intron_variant, NMD_transcript_variant | 1 | |||||
ZCCHC4 | ENST00000505412.1 | c.604+4798G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.906 AC: 137720AN: 151928Hom.: 62647 Cov.: 30
GnomAD3 genomes
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30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.907 AC: 137841AN: 152046Hom.: 62709 Cov.: 30 AF XY: 0.906 AC XY: 67337AN XY: 74318
GnomAD4 genome
?
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137841
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152046
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30
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67337
AN XY:
74318
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2828
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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