4-83421714-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_133636.5(HELQ):c.2798A>G(p.Asn933Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,330 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_133636.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HELQ | NM_133636.5 | c.2798A>G | p.Asn933Ser | missense_variant | 15/18 | ENST00000295488.8 | |
HELQ | NM_001297755.2 | c.2597A>G | p.Asn866Ser | missense_variant | 14/17 | ||
HELQ | NM_001297756.2 | c.1307A>G | p.Asn436Ser | missense_variant | 15/18 | ||
HELQ | NM_001297757.2 | c.1166A>G | p.Asn389Ser | missense_variant | 14/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HELQ | ENST00000295488.8 | c.2798A>G | p.Asn933Ser | missense_variant | 15/18 | 1 | NM_133636.5 | P1 | |
HELQ | ENST00000510985.1 | c.2597A>G | p.Asn866Ser | missense_variant | 14/17 | 1 | |||
HELQ | ENST00000508591.5 | c.*1230A>G | 3_prime_UTR_variant, NMD_transcript_variant | 14/17 | 1 | ||||
HELQ | ENST00000512539.1 | n.286A>G | non_coding_transcript_exon_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152242Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000440 AC: 11AN: 249788Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135030
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460970Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 726782
GnomAD4 genome ? AF: 0.00000656 AC: 1AN: 152360Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74510
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2022 | The c.2798A>G (p.N933S) alteration is located in exon 15 (coding exon 15) of the HELQ gene. This alteration results from a A to G substitution at nucleotide position 2798, causing the asparagine (N) at amino acid position 933 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at