chr8-79766258-AGGCATGT-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001282851.2(HEY1):c.-2_5delACATGCC(p.Met1fs) variant causes a frameshift, start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 1,530,764 control chromosomes in the GnomAD database, including 11,511 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001282851.2 frameshift, start_lost
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HEY1 | NM_012258.4 | c.331+386_331+392delACATGCC | intron_variant | Intron 4 of 4 | ENST00000354724.8 | NP_036390.3 | ||
HEY1 | NM_001282851.2 | c.-2_5delACATGCC | p.Met1fs | frameshift_variant, start_lost | Exon 1 of 2 | NP_001269780.1 | ||
HEY1 | NM_001282851.2 | c.-2_5delACATGCC | 5_prime_UTR_variant | Exon 1 of 2 | NP_001269780.1 | |||
HEY1 | NM_001040708.2 | c.343+386_343+392delACATGCC | intron_variant | Intron 4 of 4 | NP_001035798.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.124 AC: 18786AN: 152010Hom.: 1274 Cov.: 31
GnomAD3 exomes AF: 0.0733 AC: 8601AN: 117348Hom.: 704 AF XY: 0.0841 AC XY: 5386AN XY: 64036
GnomAD4 exome AF: 0.113 AC: 155102AN: 1378634Hom.: 10241 AF XY: 0.117 AC XY: 79646AN XY: 680170
GnomAD4 genome AF: 0.123 AC: 18784AN: 152130Hom.: 1270 Cov.: 31 AF XY: 0.126 AC XY: 9375AN XY: 74386
ClinVar
Submissions by phenotype
HEY1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at