chr1-41510659-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_024503.5(HIVEP3):c.7013C>T(p.Pro2338Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00504 in 1,526,972 control chromosomes in the GnomAD database, including 330 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. P2338P) has been classified as Likely benign.
Frequency
Consequence
NM_024503.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIVEP3 | NM_024503.5 | c.7013C>T | p.Pro2338Leu | missense_variant | 9/9 | ENST00000372583.6 | |
HIVEP3 | NM_001127714.3 | c.7010C>T | p.Pro2337Leu | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIVEP3 | ENST00000372583.6 | c.7013C>T | p.Pro2338Leu | missense_variant | 9/9 | 1 | NM_024503.5 | P5 | |
HIVEP3 | ENST00000372584.5 | c.7010C>T | p.Pro2337Leu | missense_variant | 8/8 | 1 | A2 | ||
HIVEP3 | ENST00000643665.1 | c.7010C>T | p.Pro2337Leu | missense_variant | 8/8 | A2 | |||
HIVEP3 | ENST00000460604.1 | n.1940C>T | non_coding_transcript_exon_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0260 AC: 3956AN: 152162Hom.: 183 Cov.: 33
GnomAD3 exomes AF: 0.00618 AC: 834AN: 135002Hom.: 28 AF XY: 0.00505 AC XY: 366AN XY: 72510
GnomAD4 exome AF: 0.00272 AC: 3737AN: 1374692Hom.: 147 Cov.: 34 AF XY: 0.00238 AC XY: 1608AN XY: 675394
GnomAD4 genome ? AF: 0.0260 AC: 3961AN: 152280Hom.: 183 Cov.: 33 AF XY: 0.0257 AC XY: 1914AN XY: 74470
ClinVar
Submissions by phenotype
HIVEP3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 23, 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