rs12975585

Positions:

• chr19-41264326-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• 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]

ACMG classification

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: 64069 AN: 152030 Hom.: 14461 Cov.: 34

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.391

GnomAD4 exome AF: 0.358 AC: 117552 AN: 328000 Hom.: 21920 Cov.: 5 AF XY: 0.358 AC XY: 59418 AN XY: 165932

Gnomad4 AFR exome AF: 0.576

Gnomad4 AMR exome AF: 0.301

Gnomad4 ASJ exome AF: 0.283

Gnomad4 EAS exome AF: 0.273

Gnomad4 SAS exome AF: 0.346

Gnomad4 FIN exome AF: 0.363

Gnomad4 NFE exome AF: 0.363

Gnomad4 OTH exome AF: 0.376

GnomAD4 genome AF: 0.422 AC: 64136 AN: 152150 Hom.: 14495 Cov.: 34 AF XY: 0.419 AC XY: 31134 AN XY: 74392

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.387

Alfa AF: 0.395 Hom.: 1534

Bravo AF: 0.426

Asia WGS AF: 0.388 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12975585; hg19: chr19-41770231; COSMIC: COSV54567249; COSMIC: COSV54567249;