chr1-41580942-G-T

Position:

chr1-41580942-G-T

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_024503.5(HIVEP3):c.3856C>A(p.Arg1286Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 1,611,188 control chromosomes in the GnomAD database, including 48,896 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 3079 hom., cov: 33)

Exomes 𝑓: 0.24 ( 45817 hom. )

Consequence

HIVEP3
NM_024503.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.83

Variant links:

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]

HIVEP3 links:

HIVEP3 (HGNC:):

HIVEP3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 1-41580942-G-T is Benign according to our data. Variant chr1-41580942-G-T is described in ClinVar as [Benign]. Clinvar id is 402944.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.83 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HIVEP3	NM_024503.5 linkuse as main transcript	c.3856C>A	p.Arg1286Arg	synonymous_variant	4/9	ENST00000372583.6	NP_078779.2	Q5T1R4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
HIVEP3	ENST00000372583.6 linkuse as main transcript	c.3856C>A	p.Arg1286Arg	synonymous_variant	4/9	1	NM_024503.5	ENSP00000361664.1	Q5T1R4-1
HIVEP3	ENST00000372584.5 linkuse as main transcript	c.3856C>A	p.Arg1286Arg	synonymous_variant	3/8	1		ENSP00000361665.1	Q5T1R4-2
HIVEP3	ENST00000643665.1 linkuse as main transcript	c.3856C>A	p.Arg1286Arg	synonymous_variant	3/8			ENSP00000494598.1	Q5T1R4-2

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27498

AN:

152034

Hom.:

3079

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0560

Gnomad AMI

AF:

0.365

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.171

Gnomad EAS

AF:

0.0484

Gnomad SAS

AF:

0.181

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.266

Gnomad OTH

AF:

0.173

GnomAD3 exomes

AF:

0.190

AC:

46940

AN:

247584

Hom.:

5310

AF XY:

0.196

AC XY:

26115

AN XY:

133572

show subpopulations

Gnomad AFR exome

AF:

0.0487

Gnomad AMR exome

AF:

0.0981

Gnomad ASJ exome

AF:

0.167

Gnomad EAS exome

AF:

0.0479

Gnomad SAS exome

AF:

0.183

Gnomad FIN exome

AF:

0.231

Gnomad NFE exome

AF:

0.257

Gnomad OTH exome

AF:

0.201

GnomAD4 exome

AF:

0.243

AC:

354134

AN:

1459038

Hom.:

45817

Cov.:

AF XY:

0.241

AC XY:

174809

AN XY:

725536

show subpopulations

Gnomad4 AFR exome

AF:

0.0436

Gnomad4 AMR exome

AF:

0.104

Gnomad4 ASJ exome

AF:

0.165

Gnomad4 EAS exome

AF:

0.0605

Gnomad4 SAS exome

AF:

0.179

Gnomad4 FIN exome

AF:

0.228

Gnomad4 NFE exome

AF:

0.270

Gnomad4 OTH exome

AF:

0.226

GnomAD4 genome

AF:

0.181

AC:

27485

AN:

152150

Hom.:

3079

Cov.:

AF XY:

0.177

AC XY:

13163

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.0558

Gnomad4 AMR

AF:

0.142

Gnomad4 ASJ

AF:

0.171

Gnomad4 EAS

AF:

0.0485

Gnomad4 SAS

AF:

0.181

Gnomad4 FIN

AF:

0.235

Gnomad4 NFE

AF:

0.266

Gnomad4 OTH

AF:

0.171

Alfa

AF:

0.209

Hom.:

2012

Bravo

AF:

0.167

Asia WGS

AF:

0.129

AC:

451

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

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, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 31, 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). -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

3.8

DANN

Benign

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over