rs10516510
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_125926.1(CXXC4-AS1):n.96+25145G>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 0.254 in 151,906 control chromosomes in the GnomAD database, including 5,043 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 0.25 ( 5043 hom., cov: 33)
Consequence
CXXC4-AS1
NR_125926.1 intron, non_coding_transcript
NR_125926.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.210
Genes affected
CXXC4-AS1 (HGNC:41054): (CXXC4 antisense RNA 1)
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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=-0.92).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CXXC4-AS1 | NR_125926.1 | n.96+25145G>A | intron_variant, non_coding_transcript_variant | |||||
LOC124900745 | XR_007058211.1 | n.3174-128C>T | intron_variant, non_coding_transcript_variant | |||||
LOC124900745 | XR_007058210.1 | n.1564-128C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CXXC4-AS1 | ENST00000500179.1 | n.96+25145G>A | intron_variant, non_coding_transcript_variant | 2 | ||||||
CXXC4-AS1 | ENST00000664466.1 | n.212+25145G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.254 AC: 38595AN: 151788Hom.: 5044 Cov.: 33
GnomAD3 genomes
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.254 AC: 38598AN: 151906Hom.: 5043 Cov.: 33 AF XY: 0.259 AC XY: 19192AN XY: 74220
GnomAD4 genome
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33
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19192
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935
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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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at