19-41302527-A-T

Position:

• chr19-41302527-A-T

Variant summary

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

The NM_007040.6(HNRNPUL1):​c.1688-138A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,128,630 control chromosomes in the GnomAD database, including 13,417 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 0.14 (1667 hom., cov: 31)
  • Exomes 𝑓: 0.15 (11750 hom.)
• Consequence: HNRNPUL1 NM_007040.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

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]

HNRNPUL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HNRNPUL1	NM_007040.6	c.1688-138A>T		intron_variant		ENST00000392006.8	NP_008971.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HNRNPUL1	ENST00000392006.8	c.1688-138A>T		intron_variant		1	NM_007040.6	ENSP00000375863.2

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20955 AN: 151852 Hom.: 1671 Cov.: 31

Gnomad AFR AF: 0.0831

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.0833

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.158

GnomAD3 exomes AF: 0.142 AC: 28758 AN: 202316 Hom.: 2367 AF XY: 0.140 AC XY: 15539 AN XY: 110634

Gnomad AFR exome AF: 0.0811

Gnomad AMR exome AF: 0.102

Gnomad ASJ exome AF: 0.153

Gnomad EAS exome AF: 0.284

Gnomad SAS exome AF: 0.0773

Gnomad FIN exome AF: 0.149

Gnomad NFE exome AF: 0.156

Gnomad OTH exome AF: 0.151

GnomAD4 exome AF: 0.150 AC: 146777 AN: 976660 Hom.: 11750 Cov.: 13 AF XY: 0.148 AC XY: 74553 AN XY: 503684

Gnomad4 AFR exome AF: 0.0805

Gnomad4 AMR exome AF: 0.105

Gnomad4 ASJ exome AF: 0.154

Gnomad4 EAS exome AF: 0.224

Gnomad4 SAS exome AF: 0.0792

Gnomad4 FIN exome AF: 0.151

Gnomad4 NFE exome AF: 0.158

Gnomad4 OTH exome AF: 0.162

GnomAD4 genome AF: 0.138 AC: 20945 AN: 151970 Hom.: 1667 Cov.: 31 AF XY: 0.135 AC XY: 10060 AN XY: 74264

Gnomad4 AFR AF: 0.0830

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.0831

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.157

Alfa AF: 0.105 Hom.: 205

Bravo AF: 0.139

Asia WGS AF: 0.186 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.50
DANN	Benign	0.37

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: rs11881940; hg19: chr19-41808432; COSMIC: COSV54559943; COSMIC: COSV54559943;