chr11-94064453-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001098672.2(HEPHL1):c.751A>G(p.Asn251Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.987 in 1,612,948 control chromosomes in the GnomAD database, including 787,298 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001098672.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HEPHL1 | NM_001098672.2 | c.751A>G | p.Asn251Asp | missense_variant | 4/20 | ENST00000315765.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HEPHL1 | ENST00000315765.10 | c.751A>G | p.Asn251Asp | missense_variant | 4/20 | 5 | NM_001098672.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.928 AC: 141071AN: 152096Hom.: 66340 Cov.: 32
GnomAD3 exomes AF: 0.981 AC: 244138AN: 248760Hom.: 120298 AF XY: 0.986 AC XY: 133103AN XY: 134968
GnomAD4 exome AF: 0.993 AC: 1450098AN: 1460734Hom.: 720918 Cov.: 36 AF XY: 0.994 AC XY: 722114AN XY: 726662
GnomAD4 genome ? AF: 0.927 AC: 141171AN: 152214Hom.: 66380 Cov.: 32 AF XY: 0.931 AC XY: 69251AN XY: 74414
ClinVar
Submissions by phenotype
Pili torti-developmental delay-neurological abnormalities syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
HEPHL1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 06, 2019 | This variant is classified as 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