chr1-41510461-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_024503.5(HIVEP3):c.7211C>G(p.Pro2404Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00512 in 1,501,116 control chromosomes in the GnomAD database, including 361 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 (★).
Frequency
Genomes: 𝑓 0.027 ( 203 hom., cov: 33)
Exomes 𝑓: 0.0026 ( 158 hom. )
Consequence
HIVEP3
NM_024503.5 missense
NM_024503.5 missense
Scores
11
Clinical Significance
Conservation
PhyloP100: 0.0340
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0017612576).
BP6
?
Variant 1-41510461-G-C is Benign according to our data. Variant chr1-41510461-G-C is described in ClinVar as [Benign]. Clinvar id is 3037152.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0918 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIVEP3 | NM_024503.5 | c.7211C>G | p.Pro2404Arg | missense_variant | 9/9 | ENST00000372583.6 | |
HIVEP3 | NM_001127714.3 | c.7208C>G | p.Pro2403Arg | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIVEP3 | ENST00000372583.6 | c.7211C>G | p.Pro2404Arg | missense_variant | 9/9 | 1 | NM_024503.5 | P5 | |
HIVEP3 | ENST00000372584.5 | c.7208C>G | p.Pro2403Arg | missense_variant | 8/8 | 1 | A2 | ||
HIVEP3 | ENST00000643665.1 | c.7208C>G | p.Pro2403Arg | missense_variant | 8/8 | A2 | |||
HIVEP3 | ENST00000460604.1 | n.2138C>G | non_coding_transcript_exon_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0272 AC: 4139AN: 152106Hom.: 203 Cov.: 33
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GnomAD3 exomes AF: 0.00751 AC: 1230AN: 163864Hom.: 52 AF XY: 0.00576 AC XY: 505AN XY: 87674
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GnomAD4 exome AF: 0.00262 AC: 3538AN: 1348894Hom.: 158 Cov.: 29 AF XY: 0.00234 AC XY: 1542AN XY: 659864
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GnomAD4 genome ? AF: 0.0272 AC: 4144AN: 152222Hom.: 203 Cov.: 33 AF XY: 0.0269 AC XY: 2001AN XY: 74446
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N
PrimateAI
Benign
T
Polyphen
B;B;B
Vest4
0.048, 0.11
MVP
0.061
MPC
0.76
ClinPred
T
GERP RS
Varity_R
gMVP
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