chr1-41511257-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_024503.5(HIVEP3):c.6415G>A(p.Glu2139Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000442 in 1,602,634 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_024503.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIVEP3 | NM_024503.5 | c.6415G>A | p.Glu2139Lys | missense_variant | 9/9 | ENST00000372583.6 | |
HIVEP3 | NM_001127714.3 | c.6412G>A | p.Glu2138Lys | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIVEP3 | ENST00000372583.6 | c.6415G>A | p.Glu2139Lys | missense_variant | 9/9 | 1 | NM_024503.5 | P5 | |
HIVEP3 | ENST00000372584.5 | c.6412G>A | p.Glu2138Lys | missense_variant | 8/8 | 1 | A2 | ||
HIVEP3 | ENST00000643665.1 | c.6412G>A | p.Glu2138Lys | missense_variant | 8/8 | A2 | |||
HIVEP3 | ENST00000460604.1 | n.1342G>A | non_coding_transcript_exon_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00225 AC: 342AN: 152114Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000678 AC: 162AN: 238854Hom.: 0 AF XY: 0.000488 AC XY: 63AN XY: 129112
GnomAD4 exome AF: 0.000253 AC: 367AN: 1450402Hom.: 5 Cov.: 33 AF XY: 0.000190 AC XY: 137AN XY: 719958
GnomAD4 genome ? AF: 0.00225 AC: 342AN: 152232Hom.: 1 Cov.: 32 AF XY: 0.00214 AC XY: 159AN XY: 74440
ClinVar
Submissions by phenotype
HIVEP3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 09, 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