4-185020281-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001300781.2(HELT):c.238C>G(p.Leu80Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,986 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L80P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001300781.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HELT | NM_001300781.2 | c.238C>G | p.Leu80Val | missense_variant | Exon 4 of 4 | ENST00000515777.6 | NP_001287710.1 | |
HELT | NM_001300782.2 | c.235C>G | p.Leu79Val | missense_variant | Exon 4 of 4 | NP_001287711.1 | ||
HELT | XM_017008186.2 | c.406C>G | p.Leu136Val | missense_variant | Exon 4 of 4 | XP_016863675.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HELT | ENST00000515777.6 | c.238C>G | p.Leu80Val | missense_variant | Exon 4 of 4 | 1 | NM_001300781.2 | ENSP00000426033.1 | ||
HELT | ENST00000338875.5 | c.493C>G | p.Leu165Val | missense_variant | Exon 4 of 4 | 1 | ENSP00000343464.4 | |||
HELT | ENST00000505610.5 | c.235C>G | p.Leu79Val | missense_variant | Exon 4 of 4 | 1 | ENSP00000422140.1 | |||
HELT | ENST00000513599.1 | n.578C>G | non_coding_transcript_exon_variant | Exon 3 of 3 | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250408Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135470
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460986Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726670
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.493C>G (p.L165V) alteration is located in exon 4 (coding exon 4) of the HELT gene. This alteration results from a C to G substitution at nucleotide position 493, causing the leucine (L) at amino acid position 165 to be replaced by a valine (V). 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