4-83427612-T-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_133636.5(HELQ):c.2627A>T(p.Tyr876Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00212 in 1,604,092 control chromosomes in the GnomAD database, including 55 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_133636.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HELQ | NM_133636.5 | c.2627A>T | p.Tyr876Phe | missense_variant | Exon 13 of 18 | ENST00000295488.8 | NP_598375.3 | |
HELQ | NM_001297755.2 | c.2426A>T | p.Tyr809Phe | missense_variant | Exon 12 of 17 | NP_001284684.2 | ||
HELQ | NM_001297756.2 | c.1136A>T | p.Tyr379Phe | missense_variant | Exon 13 of 18 | NP_001284685.1 | ||
HELQ | NM_001297757.2 | c.995A>T | p.Tyr332Phe | missense_variant | Exon 12 of 17 | NP_001284686.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0115 AC: 1753AN: 152184Hom.: 27 Cov.: 32
GnomAD3 exomes AF: 0.00295 AC: 713AN: 241480Hom.: 14 AF XY: 0.00192 AC XY: 251AN XY: 130856
GnomAD4 exome AF: 0.00113 AC: 1636AN: 1451790Hom.: 26 Cov.: 29 AF XY: 0.000982 AC XY: 709AN XY: 722184
GnomAD4 genome AF: 0.0116 AC: 1769AN: 152302Hom.: 29 Cov.: 32 AF XY: 0.0112 AC XY: 835AN XY: 74488
ClinVar
Submissions by phenotype
HELQ-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at