chr20-63560222-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001037335.2(HELZ2):c.7606C>T(p.Arg2536Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000886 in 1,535,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001037335.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HELZ2 | NM_001037335.2 | c.7606C>T | p.Arg2536Trp | missense_variant | 18/20 | ENST00000467148.2 | NP_001032412.2 | |
HELZ2 | NM_033405.3 | c.5899C>T | p.Arg1967Trp | missense_variant | 12/14 | NP_208384.3 | ||
HELZ2 | XM_024452006.2 | c.7690C>T | p.Arg2564Trp | missense_variant | 16/18 | XP_024307774.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HELZ2 | ENST00000467148.2 | c.7606C>T | p.Arg2536Trp | missense_variant | 18/20 | 1 | NM_001037335.2 | ENSP00000417401 | P1 | |
HELZ2 | ENST00000427522.6 | c.5899C>T | p.Arg1967Trp | missense_variant | 12/14 | 1 | ENSP00000393257 | |||
HELZ2 | ENST00000478861.1 | n.559+367C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000812 AC: 12AN: 147858Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000148 AC: 25AN: 169118Hom.: 0 AF XY: 0.000121 AC XY: 11AN XY: 90828
GnomAD4 exome AF: 0.0000894 AC: 124AN: 1387234Hom.: 0 Cov.: 38 AF XY: 0.0000948 AC XY: 65AN XY: 686014
GnomAD4 genome AF: 0.0000812 AC: 12AN: 147858Hom.: 0 Cov.: 32 AF XY: 0.0000555 AC XY: 4AN XY: 72104
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 07, 2023 | The c.7606C>T (p.R2536W) alteration is located in exon 18 (coding exon 17) of the HELZ2 gene. This alteration results from a C to T substitution at nucleotide position 7606, causing the arginine (R) at amino acid position 2536 to be replaced by a tryptophan (W). 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