rs1468158
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_024034.2(CLUHP3):n.871+220T>C 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 0.667 in 152,176 control chromosomes in the GnomAD database, including 34,381 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 0.67 ( 34370 hom., cov: 33)
Exomes 𝑓: 0.80 ( 11 hom. )
Consequence
CLUHP3
NR_024034.2 intron, non_coding_transcript
NR_024034.2 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.17
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=-0.93).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLUHP3 | NR_024034.2 | n.871+220T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLUHP3 | ENST00000563678.1 | n.432+220T>C | intron_variant, non_coding_transcript_variant | ||||||
ENST00000686087.1 | n.563+220T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.667 AC: 101403AN: 152028Hom.: 34354 Cov.: 33
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GnomAD4 exome AF: 0.800 AC: 24AN: 30Hom.: 11 AF XY: 0.727 AC XY: 16AN XY: 22
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GnomAD4 genome ? AF: 0.667 AC: 101469AN: 152146Hom.: 34370 Cov.: 33 AF XY: 0.660 AC XY: 49080AN XY: 74368
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ClinVar
Not reported inComputational scores
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Name
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Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at