4-83432201-A-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_133636.5(HELQ):c.2115T>G(p.Ile705Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000158 in 1,603,168 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_133636.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HELQ | NM_133636.5 | c.2115T>G | p.Ile705Met | missense_variant | 10/18 | ENST00000295488.8 | |
HELQ | NM_001297755.2 | c.1914T>G | p.Ile638Met | missense_variant | 9/17 | ||
HELQ | NM_001297756.2 | c.624T>G | p.Ile208Met | missense_variant | 10/18 | ||
HELQ | NM_001297757.2 | c.483T>G | p.Ile161Met | missense_variant | 9/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HELQ | ENST00000295488.8 | c.2115T>G | p.Ile705Met | missense_variant | 10/18 | 1 | NM_133636.5 | P1 | |
HELQ | ENST00000510985.1 | c.1914T>G | p.Ile638Met | missense_variant | 9/17 | 1 | |||
HELQ | ENST00000508591.5 | c.*547T>G | 3_prime_UTR_variant, NMD_transcript_variant | 9/17 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000841 AC: 128AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000231 AC: 57AN: 246536Hom.: 0 AF XY: 0.000172 AC XY: 23AN XY: 133552
GnomAD4 exome AF: 0.0000855 AC: 124AN: 1450852Hom.: 1 Cov.: 29 AF XY: 0.0000720 AC XY: 52AN XY: 721888
GnomAD4 genome ? AF: 0.000847 AC: 129AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.000859 AC XY: 64AN XY: 74490
ClinVar
Submissions by phenotype
HELQ-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 25, 2019 | 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