rs141449330
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP6_Very_StrongBS1
The NM_031844.3(HNRNPU):c.875C>T(p.Thr292Ile) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000402 in 1,566,688 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_031844.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HNRNPU | NM_031844.3 | c.875C>T | p.Thr292Ile | missense_variant, splice_region_variant | Exon 3 of 14 | ENST00000640218.2 | NP_114032.2 | |
HNRNPU | NM_004501.3 | c.818C>T | p.Thr273Ile | missense_variant, splice_region_variant | Exon 3 of 14 | NP_004492.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000405 AC: 6AN: 148250Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000600 AC: 15AN: 250150Hom.: 0 AF XY: 0.0000961 AC XY: 13AN XY: 135234
GnomAD4 exome AF: 0.0000402 AC: 57AN: 1418398Hom.: 0 Cov.: 30 AF XY: 0.0000481 AC XY: 34AN XY: 707488
GnomAD4 genome AF: 0.0000405 AC: 6AN: 148290Hom.: 0 Cov.: 32 AF XY: 0.0000417 AC XY: 3AN XY: 72026
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 54 Benign:1
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not provided Benign:1
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HNRNPU-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at