chr11-94067538-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001098672.2(HEPHL1):c.851T>C(p.Met284Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000062 in 1,613,532 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. M284I) has been classified as Uncertain significance.
Frequency
Consequence
NM_001098672.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HEPHL1 | NM_001098672.2 | c.851T>C | p.Met284Thr | missense_variant | 5/20 | ENST00000315765.10 | |
LOC124902735 | XR_007062840.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HEPHL1 | ENST00000315765.10 | c.851T>C | p.Met284Thr | missense_variant | 5/20 | 5 | NM_001098672.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 248950Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135050
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461386Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 726988
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74318
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2023 | HEPHL1: PM2, PP3 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at