Variant 14-21230910-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_004500.4(HNRNPC):c.317+87T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,429,018 control chromosomes in the GnomAD database, including 45,417 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 0.21 ( 4035 hom., cov: 31)

Exomes 𝑓: 0.25 ( 41382 hom. )

Consequence

HNRNPC
NM_004500.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.01

Variant links:

Genes affected

HNRNPC (HGNC:5035): (heterogeneous nuclear ribonucleoprotein C) 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 can act as a tetramer and is involved in the assembly of 40S hnRNP particles. Multiple transcript variants encoding at least two different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

HNRNPC links:

HNRNPC (HGNC:):

HNRNPC links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.35).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HNRNPC	NM_004500.4 linkuse as main transcript	c.317+87T>G		intron_variant		ENST00000553300.6	NP_004491.2	P07910-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HNRNPC	ENST00000553300.6 linkuse as main transcript	c.317+87T>G		intron_variant		1	NM_004500.4	ENSP00000450544.1		P07910-2

Frequencies

GnomAD3 genomes

AF:

0.214

AC:

32443

AN:

151948

Hom.:

4028

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0962

Gnomad AMI

AF:

0.285

Gnomad AMR

AF:

0.317

Gnomad ASJ

AF:

0.237

Gnomad EAS

AF:

0.299

Gnomad SAS

AF:

0.290

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.248

Gnomad OTH

AF:

0.209

GnomAD3 exomes

AF:

0.263

AC:

62230

AN:

236738

Hom.:

8977

AF XY:

0.262

AC XY:

33656

AN XY:

128672

show subpopulations

Gnomad AFR exome

AF:

0.0970

Gnomad AMR exome

AF:

0.388

Gnomad ASJ exome

AF:

0.235

Gnomad EAS exome

AF:

0.301

Gnomad SAS exome

AF:

0.282

Gnomad FIN exome

AF:

0.223

Gnomad NFE exome

AF:

0.250

Gnomad OTH exome

AF:

0.251

GnomAD4 exome

AF:

0.249

AC:

318170

AN:

1276952

Hom.:

41382

Cov.:

AF XY:

0.250

AC XY:

160540

AN XY:

642784

show subpopulations

Gnomad4 AFR exome

AF:

0.0910

Gnomad4 AMR exome

AF:

0.375

Gnomad4 ASJ exome

AF:

0.233

Gnomad4 EAS exome

AF:

0.283

Gnomad4 SAS exome

AF:

0.280

Gnomad4 FIN exome

AF:

0.223

Gnomad4 NFE exome

AF:

0.248

Gnomad4 OTH exome

AF:

0.233

GnomAD4 genome

AF:

0.213

AC:

32456

AN:

152066

Hom.:

4035

Cov.:

AF XY:

0.217

AC XY:

16138

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.0962

Gnomad4 AMR

AF:

0.317

Gnomad4 ASJ

AF:

0.237

Gnomad4 EAS

AF:

0.300

Gnomad4 SAS

AF:

0.289

Gnomad4 FIN

AF:

0.214

Gnomad4 NFE

AF:

0.248

Gnomad4 OTH

AF:

0.209

Alfa

AF:

0.243

Hom.:

2501

Bravo

AF:

0.216

Asia WGS

AF:

0.293

AC:

1019

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.35

CADD

Benign

DANN

Benign

0.79

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.0

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over