rs615177
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_024503.5(HIVEP3):āc.5736T>Cā(p.Ala1912=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 1,608,538 control chromosomes in the GnomAD database, including 328,493 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.65 ( 32343 hom., cov: 31)
Exomes š: 0.63 ( 296150 hom. )
Consequence
HIVEP3
NM_024503.5 synonymous
NM_024503.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.830
Genes affected
HIVEP3 (HGNC:13561): (HIVEP zinc finger 3) This gene encodes a member of the human immunodeficiency virus type 1 enhancer-binding protein family. Members of this protein family contain multiple zinc finger and acid-rich (ZAS) domains and serine-threonine rich regions. This protein acts as a transcription factor and is able to regulate nuclear factor kappaB-mediated transcription by binding the kappaB motif in target genes. This protein also binds the recombination signal sequence that flanks the V, D, and J regions of immunoglobulin and T-cell receptors. Alternate splicing results in both coding and non-coding transcript variants. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 1-41513485-A-G is Benign according to our data. Variant chr1-41513485-A-G is described in ClinVar as [Benign]. Clinvar id is 402943.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.83 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIVEP3 | NM_024503.5 | c.5736T>C | p.Ala1912= | synonymous_variant | 8/9 | ENST00000372583.6 | |
HIVEP3 | NM_001127714.3 | c.5736T>C | p.Ala1912= | synonymous_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIVEP3 | ENST00000372583.6 | c.5736T>C | p.Ala1912= | synonymous_variant | 8/9 | 1 | NM_024503.5 | P5 | |
HIVEP3 | ENST00000372584.5 | c.5736T>C | p.Ala1912= | synonymous_variant | 7/8 | 1 | A2 | ||
HIVEP3 | ENST00000643665.1 | c.5736T>C | p.Ala1912= | synonymous_variant | 7/8 | A2 | |||
HIVEP3 | ENST00000460604.1 | n.663T>C | non_coding_transcript_exon_variant | 4/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.648 AC: 98349AN: 151752Hom.: 32315 Cov.: 31
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GnomAD3 exomes AF: 0.670 AC: 163045AN: 243254Hom.: 56083 AF XY: 0.665 AC XY: 88176AN XY: 132514
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GnomAD4 exome AF: 0.633 AC: 922403AN: 1456668Hom.: 296150 Cov.: 76 AF XY: 0.634 AC XY: 459276AN XY: 724360
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GnomAD4 genome ? AF: 0.648 AC: 98428AN: 151870Hom.: 32343 Cov.: 31 AF XY: 0.654 AC XY: 48493AN XY: 74202
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 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: Frequency - |
HIVEP3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at