Variant 4-82426156-TAAGA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_031372.4(HNRNPDL):c.1193-31_1193-28del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 1,588,816 control chromosomes in the GnomAD database, including 124,763 homozygotes. Variant has been reported in ClinVar as Benign (★). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.32 ( 9509 hom., cov: 0)

Exomes 𝑓: 0.39 ( 115254 hom. )

Consequence

HNRNPDL
NM_031372.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.85

Variant links:

Genes affected

HNRNPDL (HGNC:5037): (heterogeneous nuclear ribonucleoprotein D like) This gene belongs to the subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some seem to shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene has two RRM domains that bind to RNAs. Three alternatively spliced transcript variants have been described for this gene. One of the variants is probably not translated because the transcript is a candidate for nonsense-mediated mRNA decay. The protein isoforms encoded by this gene are similar to its family member HNRPD. [provided by RefSeq, May 2011]

HNRNPDL links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 4-82426156-TAAGA-T is Benign according to our data. Variant chr4-82426156-TAAGA-T is described in ClinVar as [Benign]. Clinvar id is 1228006.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
HNRNPDL	NM_031372.4 linkuse as main transcript	c.1193-31_1193-28del	intron_variant	ENST00000295470.10	NP_112740.1
HNRNPDL	NM_001207000.1 linkuse as main transcript	c.1022-31_1022-28del	intron_variant		NP_001193929.1
HNRNPDL	NR_003249.2 linkuse as main transcript	n.1728-31_1728-28del	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HNRNPDL	ENST00000295470.10 linkuse as main transcript	c.1193-31_1193-28del		intron_variant		1	NM_031372.4	ENSP00000295470	P4	O14979-1

Frequencies

GnomAD3 genomes

AF:

0.321

AC:

48785

AN:

151764

Hom.:

9505

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.388

Gnomad AMR

AF:

0.473

Gnomad ASJ

AF:

0.465

Gnomad EAS

AF:

0.212

Gnomad SAS

AF:

0.546

Gnomad FIN

AF:

0.441

Gnomad MID

AF:

0.420

Gnomad NFE

AF:

0.385

Gnomad OTH

AF:

0.359

GnomAD3 exomes

AF:

0.395

AC:

99139

AN:

250754

Hom.:

21163

AF XY:

0.406

AC XY:

54983

AN XY:

135542

show subpopulations

Gnomad AFR exome

AF:

0.0922

Gnomad AMR exome

AF:

0.497

Gnomad ASJ exome

AF:

0.469

Gnomad EAS exome

AF:

0.215

Gnomad SAS exome

AF:

0.538

Gnomad FIN exome

AF:

0.429

Gnomad NFE exome

AF:

0.384

Gnomad OTH exome

AF:

0.422

GnomAD4 exome

AF:

0.392

AC:

563643

AN:

1436934

Hom.:

115254

AF XY:

0.397

AC XY:

284485

AN XY:

716670

show subpopulations

Gnomad4 AFR exome

AF:

0.0937

Gnomad4 AMR exome

AF:

0.497

Gnomad4 ASJ exome

AF:

0.481

Gnomad4 EAS exome

AF:

0.175

Gnomad4 SAS exome

AF:

0.531

Gnomad4 FIN exome

AF:

0.428

Gnomad4 NFE exome

AF:

0.390

Gnomad4 OTH exome

AF:

0.392

GnomAD4 genome

AF:

0.321

AC:

48796

AN:

151882

Hom.:

9509

Cov.:

AF XY:

0.329

AC XY:

24443

AN XY:

74222

show subpopulations

Gnomad4 AFR

AF:

0.102

Gnomad4 AMR

AF:

0.473

Gnomad4 ASJ

AF:

0.465

Gnomad4 EAS

AF:

0.212

Gnomad4 SAS

AF:

0.548

Gnomad4 FIN

AF:

0.441

Gnomad4 NFE

AF:

0.385

Gnomad4 OTH

AF:

0.358

Alfa

AF:

0.364

Hom.:

1987

Bravo

AF:

0.309

Asia WGS

AF:

0.381

AC:

1322

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BranchPoint Hunter

7.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over