2-196433459-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PVS1_ModerateBS1_SupportingBS2
The NM_001348768.2(HECW2):c.-35-1G>A variant causes a splice acceptor, intron change. The variant allele was found at a frequency of 0.00000975 in 1,435,750 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001348768.2 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HECW2 | NM_001348768.2 | c.-35-1G>A | splice_acceptor_variant, intron_variant | Intron 1 of 28 | ENST00000644978.2 | NP_001335697.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000261 AC: 6AN: 229964Hom.: 0 AF XY: 0.0000403 AC XY: 5AN XY: 124166
GnomAD4 exome AF: 0.00000975 AC: 14AN: 1435750Hom.: 0 Cov.: 29 AF XY: 0.0000126 AC XY: 9AN XY: 712616
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Neurodevelopmental disorder with hypotonia, seizures, and absent language Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at