rs45494802
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The XR_927402.3(ZSCAN25):n.1456-1315A>T 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 0.0247 in 151,524 control chromosomes in the GnomAD database, including 74 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 ( 74 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: 0.102
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=-0.92).
BP6
Variant 7-99735377-A-T is Benign according to our data. Variant chr7-99735377-A-T is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0247 (3740/151524) while in subpopulation NFE AF= 0.0332 (2246/67572). AF 95% confidence interval is 0.0321. There are 74 homozygotes in gnomad4. There are 1822 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 74 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZSCAN25 | XR_007059988.1 | n.1429-1315A>T | intron_variant, non_coding_transcript_variant | |||||
ZSCAN25 | XR_007059989.1 | n.1371-1315A>T | intron_variant, non_coding_transcript_variant | |||||
ZSCAN25 | XR_007059990.1 | n.1244-1315A>T | intron_variant, non_coding_transcript_variant | |||||
ZSCAN25 | XR_927402.3 | n.1456-1315A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
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Frequencies
GnomAD3 genomes AF: 0.0247 AC: 3739AN: 151408Hom.: 73 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0247 AC: 3740AN: 151524Hom.: 74 Cov.: 31 AF XY: 0.0246 AC XY: 1822AN XY: 74038
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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