Variant 9-83969995-G-GT details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_031263.4(HNRNPK):c.1361+166dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 648,324 control chromosomes in the GnomAD database, including 5,413 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.11 ( 1054 hom., cov: 30)

Exomes 𝑓: 0.13 ( 4359 hom. )

Consequence

HNRNPK
NM_031263.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.73

Variant links:

Genes affected

HNRNPK (HGNC:5044): (heterogeneous nuclear ribonucleoprotein K) 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 is located in the nucleoplasm and has three repeats of KH domains that binds to RNAs. It is distinct among other hnRNP proteins in its binding preference; it binds tenaciously to poly(C). This protein is also thought to have a role during cell cycle progession. Several alternatively spliced transcript variants have been described for this gene, however, not all of them are fully characterized. [provided by RefSeq, Jul 2008]

HNRNPK links:

HNRNPK (HGNC:):

HNRNPK links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 9-83969995-G-GT is Benign according to our data. Variant chr9-83969995-G-GT is described in ClinVar as [Benign]. Clinvar id is 1280999.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HNRNPK	NM_031263.4 linkuse as main transcript	c.1361+166dupA		intron_variant		ENST00000376263.8	NP_112553.1	P61978-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HNRNPK	ENST00000376263.8 linkuse as main transcript	c.1361+166dupA		intron_variant		1	NM_031263.4	ENSP00000365439.3		P61978-2

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16099

AN:

152090

Hom.:

1049

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0348

Gnomad AMI

AF:

0.129

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.0865

Gnomad EAS

AF:

0.119

Gnomad SAS

AF:

0.103

Gnomad FIN

AF:

0.158

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.137

Gnomad OTH

AF:

0.0957

GnomAD4 exome

AF:

0.127

AC:

63096

AN:

496116

Hom.:

4359

Cov.:

AF XY:

0.126

AC XY:

33622

AN XY:

266640

show subpopulations

Gnomad4 AFR exome

AF:

0.0352

Gnomad4 AMR exome

AF:

0.121

Gnomad4 ASJ exome

AF:

0.0866

Gnomad4 EAS exome

AF:

0.112

Gnomad4 SAS exome

AF:

0.104

Gnomad4 FIN exome

AF:

0.155

Gnomad4 NFE exome

AF:

0.138

Gnomad4 OTH exome

AF:

0.119

GnomAD4 genome

AF:

0.106

AC:

16115

AN:

152208

Hom.:

1054

Cov.:

AF XY:

0.108

AC XY:

8031

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.0348

Gnomad4 AMR

AF:

0.126

Gnomad4 ASJ

AF:

0.0865

Gnomad4 EAS

AF:

0.119

Gnomad4 SAS

AF:

0.104

Gnomad4 FIN

AF:

0.158

Gnomad4 NFE

AF:

0.137

Gnomad4 OTH

AF:

0.0947

Alfa

AF:

0.0537

Hom.:

Bravo

AF:

0.0989

Asia WGS

AF:

0.107

AC:

372

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 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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