rs1126472
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002114.4(HIVEP1):c.5744A>G(p.Gln1915Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 1,613,972 control chromosomes in the GnomAD database, including 11,695 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 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_002114.4 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 |
---|---|---|---|---|---|---|---|
HIVEP1 | NM_002114.4 | c.5744A>G | p.Gln1915Arg | missense_variant | 4/9 | ENST00000379388.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIVEP1 | ENST00000379388.7 | c.5744A>G | p.Gln1915Arg | missense_variant | 4/9 | 1 | NM_002114.4 | P2 | |
HIVEP1 | ENST00000541134.5 | c.5744A>G | p.Gln1915Arg | missense_variant | 4/9 | 5 | A2 | ||
HIVEP1 | ENST00000627968.2 | c.-560A>G | 5_prime_UTR_variant | 4/8 | 5 | ||||
HIVEP1 | ENST00000442081.6 | c.166+5605A>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.140 AC: 21238AN: 152156Hom.: 1759 Cov.: 32
GnomAD3 exomes AF: 0.120 AC: 29823AN: 249166Hom.: 2052 AF XY: 0.122 AC XY: 16517AN XY: 135210
GnomAD4 exome AF: 0.111 AC: 162252AN: 1461698Hom.: 9926 Cov.: 34 AF XY: 0.113 AC XY: 82376AN XY: 727170
GnomAD4 genome ? AF: 0.140 AC: 21283AN: 152274Hom.: 1769 Cov.: 32 AF XY: 0.138 AC XY: 10247AN XY: 74458
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at