rs12975585
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000352456.7(HNRNPUL1):c.-6+1744A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 480,150 control chromosomes in the GnomAD database, including 36,415 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 0.42 ( 14495 hom., cov: 34)
Exomes 𝑓: 0.36 ( 21920 hom. )
Consequence
HNRNPUL1
ENST00000352456.7 intron
ENST00000352456.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.175
Genes affected
HNRNPUL1 (HGNC:17011): (heterogeneous nuclear ribonucleoprotein U like 1) This gene encodes a nuclear RNA-binding protein of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. This protein binds specifically to adenovirus early-1B-55kDa oncoprotein. It may play an important role in nucleocytoplasmic RNA transport, and its function is modulated by early-1B-55kDa in adenovirus-infected cells. [provided by RefSeq, Mar 2016]
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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=-0.82).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HNRNPUL1 | NM_007040.6 | upstream_gene_variant | ENST00000392006.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HNRNPUL1 | ENST00000392006.8 | upstream_gene_variant | 1 | NM_007040.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.421 AC: 64069AN: 152030Hom.: 14461 Cov.: 34
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GnomAD4 exome AF: 0.358 AC: 117552AN: 328000Hom.: 21920 Cov.: 5 AF XY: 0.358 AC XY: 59418AN XY: 165932
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GnomAD4 genome ? AF: 0.422 AC: 64136AN: 152150Hom.: 14495 Cov.: 34 AF XY: 0.419 AC XY: 31134AN XY: 74392
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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