10-43386473-A-G

Variant summary

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

The NM_001098204.2(HNRNPF):​c.*164T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0591 in 642,706 control chromosomes in the GnomAD database, including 1,720 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 0.069 ( 496 hom., cov: 33)
Exomes 𝑓: 0.056 ( 1224 hom. )

Consequence

HNRNPF
NM_001098204.2 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.29
Variant links:
Genes affected
HNRNPF (HGNC:5039): (heterogeneous nuclear ribonucleoprotein F) This gene belongs to the subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA binding proteins that complex with heterogeneous nuclear RNA (hnRNA). These proteins are associated with pre-mRNAs in the nucleus and regulate alternative splicing, polyadenylation, 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 three repeats of quasi-RRM domains that bind to RNAs which have guanosine-rich sequences. This protein is very similar to the family member hnRPH. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HNRNPFNM_001098204.2 linkuse as main transcriptc.*164T>C 3_prime_UTR_variant 4/4 ENST00000682386.1 NP_001091674.1 P52597A0A024R7T3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HNRNPFENST00000682386.1 linkuse as main transcriptc.*164T>C 3_prime_UTR_variant 4/4 NM_001098204.2 ENSP00000507787.1 P52597

Frequencies

GnomAD3 genomes
AF:
0.0686
AC:
10448
AN:
152194
Hom.:
492
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0937
Gnomad AMI
AF:
0.00548
Gnomad AMR
AF:
0.0961
Gnomad ASJ
AF:
0.0325
Gnomad EAS
AF:
0.198
Gnomad SAS
AF:
0.0916
Gnomad FIN
AF:
0.0754
Gnomad MID
AF:
0.0411
Gnomad NFE
AF:
0.0376
Gnomad OTH
AF:
0.0649
GnomAD4 exome
AF:
0.0561
AC:
27500
AN:
490394
Hom.:
1224
Cov.:
6
AF XY:
0.0567
AC XY:
14481
AN XY:
255584
show subpopulations
Gnomad4 AFR exome
AF:
0.0929
Gnomad4 AMR exome
AF:
0.0922
Gnomad4 ASJ exome
AF:
0.0340
Gnomad4 EAS exome
AF:
0.180
Gnomad4 SAS exome
AF:
0.0814
Gnomad4 FIN exome
AF:
0.0750
Gnomad4 NFE exome
AF:
0.0365
Gnomad4 OTH exome
AF:
0.0575
GnomAD4 genome
AF:
0.0688
AC:
10474
AN:
152312
Hom.:
496
Cov.:
33
AF XY:
0.0732
AC XY:
5452
AN XY:
74474
show subpopulations
Gnomad4 AFR
AF:
0.0937
Gnomad4 AMR
AF:
0.0967
Gnomad4 ASJ
AF:
0.0325
Gnomad4 EAS
AF:
0.199
Gnomad4 SAS
AF:
0.0919
Gnomad4 FIN
AF:
0.0754
Gnomad4 NFE
AF:
0.0376
Gnomad4 OTH
AF:
0.0652
Alfa
AF:
0.0438
Hom.:
194
Bravo
AF:
0.0710
Asia WGS
AF:
0.145
AC:
502
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.43
CADD
Benign
15
DANN
Benign
0.92

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: rs10409; hg19: chr10-43881921; API