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GeneBe

rs17197037

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004500.4(HNRNPC):c.-37+5816C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,686 control chromosomes in the GnomAD database, including 10,597 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 0.36 ( 10597 hom., cov: 30)

Consequence

HNRNPC
NM_004500.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.487
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HNRNPCNM_004500.4 linkuse as main transcriptc.-37+5816C>T intron_variant ENST00000553300.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HNRNPCENST00000553300.6 linkuse as main transcriptc.-37+5816C>T intron_variant 1 NM_004500.4 P3P07910-2

Frequencies

GnomAD3 genomes
AF:
0.364
AC:
55102
AN:
151566
Hom.:
10595
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.275
Gnomad AMI
AF:
0.429
Gnomad AMR
AF:
0.345
Gnomad ASJ
AF:
0.523
Gnomad EAS
AF:
0.689
Gnomad SAS
AF:
0.390
Gnomad FIN
AF:
0.323
Gnomad MID
AF:
0.453
Gnomad NFE
AF:
0.390
Gnomad OTH
AF:
0.414
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.363
AC:
55109
AN:
151686
Hom.:
10597
Cov.:
30
AF XY:
0.361
AC XY:
26709
AN XY:
74086
show subpopulations
Gnomad4 AFR
AF:
0.274
Gnomad4 AMR
AF:
0.344
Gnomad4 ASJ
AF:
0.523
Gnomad4 EAS
AF:
0.688
Gnomad4 SAS
AF:
0.391
Gnomad4 FIN
AF:
0.323
Gnomad4 NFE
AF:
0.390
Gnomad4 OTH
AF:
0.418
Alfa
AF:
0.401
Hom.:
23593
Bravo
AF:
0.363
Asia WGS
AF:
0.471
AC:
1639
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
3.2
Dann
Benign
0.51

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.

Other links and lift over

dbSNP: rs17197037; hg19: chr14-21725654; API