chr19-41279377-T-G

Variant names:

• chr19-41279377-T-G
• rs3745295
• NM_007040.6:c.886+201T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HNRNPUL1	NM_007040.6	c.886+201T>G		intron_variant	Intron 6 of 14	ENST00000392006.8	NP_008971.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HNRNPUL1	ENST00000392006.8	c.886+201T>G		intron_variant	Intron 6 of 14	1	NM_007040.6	ENSP00000375863.2

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

African (AFR) AF: 0.277 AC: 11503 AN: 41502

American (AMR) AF: 0.178 AC: 2722 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3468

East Asian (EAS) AF: 0.345 AC: 1784 AN: 5176

South Asian (SAS) AF: 0.169 AC: 814 AN: 4824

European-Finnish (FIN) AF: 0.144 AC: 1525 AN: 10606

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.162 AC: 11023 AN: 67994

Other (OTH) AF: 0.207 AC: 438 AN: 2114

Alfa AF: 0.170 Hom.: 3840

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
PhyloP100		0.40
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3745295; hg19: chr19-41785282;