Genetic Variant HNRNPUL1:c.-6+1744A>T (chr19-41264326-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001439172.1(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
NM_001439172.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.175

Publications

14 publications found

Variant links:

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 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001439172.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein	UniProt
HNRNPUL1	NM_001439172.1	c.-6+1744A>T	intron	N/A	NP_001426101.1
HNRNPUL1	NM_144732.5	c.-6+1744A>T	intron	N/A	NP_653333.1	Q9BUJ2-4
HNRNPUL1	NM_001439179.1	c.-6+1744A>T	intron	N/A	NP_001426108.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
HNRNPUL1	ENST00000352456.7	TSL:1	c.-6+1744A>T	intron	N/A	ENSP00000340857.3	A0A0A0MRA5
HNRNPUL1	ENST00000599719.5	TSL:1	c.-6+1310A>T	intron	N/A	ENSP00000470172.1	M0QYZ0
HNRNPUL1	ENST00000851914.1		c.-70-108A>T	intron	N/A	ENSP00000521973.1

Frequencies

GnomAD3 genomes

AF:

0.421

AC:

64069

AN:

152030

Hom.:

14461

Cov.:

show subpopulations

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.:

AF XY:

0.358

AC XY:

59418

AN XY:

165932

show subpopulations

African (AFR)

AF:

0.576

AC:

4810

AN:

8348

American (AMR)

AF:

0.301

AC:

2492

AN:

8284

Ashkenazi Jewish (ASJ)

AF:

0.283

AC:

2805

AN:

9902

East Asian (EAS)

AF:

0.273

AC:

6400

AN:

23418

South Asian (SAS)

AF:

0.346

AC:

3289

AN:

9494

European-Finnish (FIN)

AF:

0.363

AC:

7878

AN:

21702

Middle Eastern (MID)

AF:

0.376

AC:

550

AN:

1462

European-Non Finnish (NFE)

AF:

0.363

AC:

82106

AN:

226202

Other (OTH)

AF:

0.376

AC:

7222

AN:

19188

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

3776

7552

11328

15104

18880

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1178

2356

3534

4712

5890

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.422

AC:

64136

AN:

152150

Hom.:

14495

Cov.:

AF XY:

0.419

AC XY:

31134

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.581

AC:

24099

AN:

41508

American (AMR)

AF:

0.324

AC:

4954

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.305

AC:

1060

AN:

3472

East Asian (EAS)

AF:

0.363

AC:

1873

AN:

5162

South Asian (SAS)

AF:

0.374

AC:

1806

AN:

4832

European-Finnish (FIN)

AF:

0.355

AC:

3764

AN:

10592

Middle Eastern (MID)

AF:

0.361

AC:

106

AN:

294

European-Non Finnish (NFE)

AF:

0.370

AC:

25133

AN:

67974

Other (OTH)

AF:

0.387

AC:

815

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1904

3809

5713

7618

9522

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

592

1184

1776

2368

2960

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.73

PhyloP100

0.17

PromoterAI

0.079

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over