rs555895621
Positions:
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_031844.3(HNRNPU):āc.429T>Cā(p.Asp143=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000998 in 1,612,704 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.000066 ( 0 hom., cov: 32)
Exomes š: 0.00010 ( 0 hom. )
Consequence
HNRNPU
NM_031844.3 synonymous
NM_031844.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.253
Genes affected
HNRNPU (HGNC:5048): (heterogeneous nuclear ribonucleoprotein U) This gene encodes a member of a family of proteins that bind nucleic acids and function in the formation of ribonucleoprotein complexes in the nucleus with heterogeneous nuclear RNA (hnRNA). The encoded protein has affinity for both RNA and DNA, and binds scaffold-attached region (SAR) DNA. Mutations in this gene have been associated with epileptic encephalopathy, early infantile, 54. A pseudogene of this gene has been identified on chromosome 14. [provided by RefSeq, Jun 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant 1-244863879-A-G is Benign according to our data. Variant chr1-244863879-A-G is described in ClinVar as [Benign]. Clinvar id is 446405.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.253 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0000662 (10/151160) while in subpopulation SAS AF= 0.00168 (8/4774). AF 95% confidence interval is 0.000834. There are 0 homozygotes in gnomad4. There are 7 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HNRNPU | NM_031844.3 | c.429T>C | p.Asp143= | synonymous_variant | 1/14 | ENST00000640218.2 | |
HNRNPU | NM_004501.3 | c.429T>C | p.Asp143= | synonymous_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HNRNPU | ENST00000640218.2 | c.429T>C | p.Asp143= | synonymous_variant | 1/14 | 1 | NM_031844.3 | P3 | |
ENST00000610145.2 | n.98A>G | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000662 AC: 10AN: 151042Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000185 AC: 46AN: 248746Hom.: 0 AF XY: 0.000222 AC XY: 30AN XY: 135002
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GnomAD4 exome AF: 0.000103 AC: 151AN: 1461544Hom.: 0 Cov.: 34 AF XY: 0.000140 AC XY: 102AN XY: 727096
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GnomAD4 genome ? AF: 0.0000662 AC: 10AN: 151160Hom.: 0 Cov.: 32 AF XY: 0.0000948 AC XY: 7AN XY: 73878
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
heterogeneous nuclear ribonucleoprotein G, human Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 09, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at