rs11568824
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The XR_927402.3(ZSCAN25):n.1456-1308C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.025 in 151,594 control chromosomes in the GnomAD database, including 78 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.025 ( 78 hom., cov: 31)
Consequence
ZSCAN25
XR_927402.3 intron, non_coding_transcript
XR_927402.3 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.113
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
?
Variant 7-99735384-C-A is Benign according to our data. Variant chr7-99735384-C-A is described in Lovd as [Likely_benign].
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.025 (3785/151594) while in subpopulation NFE AF= 0.0336 (2273/67618). AF 95% confidence interval is 0.0325. There are 78 homozygotes in gnomad4. There are 1844 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 77 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZSCAN25 | XR_007059988.1 | n.1429-1308C>A | intron_variant, non_coding_transcript_variant | ||||
ZSCAN25 | XR_007059989.1 | n.1371-1308C>A | intron_variant, non_coding_transcript_variant | ||||
ZSCAN25 | XR_007059990.1 | n.1244-1308C>A | intron_variant, non_coding_transcript_variant | ||||
ZSCAN25 | XR_927402.3 | n.1456-1308C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.0250 AC: 3784AN: 151476Hom.: 77 Cov.: 31
GnomAD3 genomes
?
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0250 AC: 3785AN: 151594Hom.: 78 Cov.: 31 AF XY: 0.0249 AC XY: 1844AN XY: 74072
GnomAD4 genome
?
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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