1-244856720-C-T
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_031844.3(HNRNPU):c.1743+8G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,457,930 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_031844.3 splice_region, intron
Scores
Clinical Significance
Conservation
Publications
- complex neurodevelopmental disorderInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- developmental and epileptic encephalopathy, 54Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HNRNPU | NM_031844.3 | c.1743+8G>A | splice_region_variant, intron_variant | Intron 9 of 13 | ENST00000640218.2 | NP_114032.2 | ||
HNRNPU | NM_004501.3 | c.1686+8G>A | splice_region_variant, intron_variant | Intron 9 of 13 | NP_004492.2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD2 exomes AF: 0.00000404 AC: 1AN: 247774 AF XY: 0.00000747 show subpopulations
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1457930Hom.: 0 Cov.: 31 AF XY: 0.00000552 AC XY: 4AN XY: 725124 show subpopulations
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 54 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at