rs200952460
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 3P and 16B. PM2PP2BP4_StrongBP6_Very_StrongBS1
The NM_031844.3(HNRNPU):āc.83A>Gā(p.Lys28Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000193 in 1,612,914 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_031844.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HNRNPU | NM_031844.3 | c.83A>G | p.Lys28Arg | missense_variant | 1/14 | ENST00000640218.2 | |
HNRNPU | NM_004501.3 | c.83A>G | p.Lys28Arg | missense_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HNRNPU | ENST00000640218.2 | c.83A>G | p.Lys28Arg | missense_variant | 1/14 | 1 | NM_031844.3 | P3 | |
ENST00000610145.2 | n.444T>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000154 AC: 38AN: 245976Hom.: 0 AF XY: 0.000156 AC XY: 21AN XY: 134202
GnomAD4 exome AF: 0.000196 AC: 287AN: 1460586Hom.: 0 Cov.: 34 AF XY: 0.000202 AC XY: 147AN XY: 726588
GnomAD4 genome ? AF: 0.000158 AC: 24AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74488
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 02, 2017 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Developmental and epileptic encephalopathy, 54 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | HNRNPU: PP2, BS1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at