rs3745295

Positions:

• chr19-41279377-T-G

Variant summary

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

The NM_007040.6(HNRNPUL1):​c.886+201T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,166 control chromosomes in the GnomAD database, including 3,491 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 0.20 (3491 hom., cov: 32)
• Consequence: HNRNPUL1 NM_007040.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398

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 (EAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HNRNPUL1	NM_007040.6	c.886+201T>G		intron_variant		ENST00000392006.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HNRNPUL1	ENST00000392006.8	c.886+201T>G		intron_variant		1	NM_007040.6	P1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30831 AN: 152048 Hom.: 3477 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.208

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.203 AC: 30870 AN: 152166 Hom.: 3491 Cov.: 32 AF XY: 0.202 AC XY: 15020 AN XY: 74390

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.207

Alfa AF: 0.168 Hom.: 2882

Bravo AF: 0.213

Asia WGS AF: 0.287 AC: 997 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	8.1
DANN	Benign	0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3745295; hg19: chr19-41785282;