10-43386473-A-G
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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
NM_001098204.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.29
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]
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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=-0.43).
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 |
---|---|---|---|---|---|---|---|---|
HNRNPF | NM_001098204.2 | c.*164T>C | 3_prime_UTR_variant | 4/4 | ENST00000682386.1 | NP_001091674.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HNRNPF | ENST00000682386.1 | c.*164T>C | 3_prime_UTR_variant | 4/4 | NM_001098204.2 | ENSP00000507787.1 |
Frequencies
GnomAD3 genomes AF: 0.0686 AC: 10448AN: 152194Hom.: 492 Cov.: 33
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GnomAD4 exome AF: 0.0561 AC: 27500AN: 490394Hom.: 1224 Cov.: 6 AF XY: 0.0567 AC XY: 14481AN XY: 255584
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GnomAD4 genome AF: 0.0688 AC: 10474AN: 152312Hom.: 496 Cov.: 33 AF XY: 0.0732 AC XY: 5452AN XY: 74474
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at