1-41581141-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_024503.5(HIVEP3):c.3657G>A(p.Gln1219Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.996 in 1,548,154 control chromosomes in the GnomAD database, including 768,319 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.98 ( 73060 hom., cov: 29)

Exomes 𝑓: 1.0 ( 695259 hom. )

Consequence

HIVEP3
NM_024503.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.387

Publications

11 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 1-41581141-C-T is Benign according to our data. Variant chr1-41581141-C-T is described in ClinVar as Benign. ClinVar VariationId is 402945.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.387 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HIVEP3	NM_024503.5 link	c.3657G>A	p.Gln1219Gln	synonymous_variant	Exon 4 of 9	ENST00000372583.6	NP_078779.2
HIVEP3	NM_001127714.3 link	c.3657G>A	p.Gln1219Gln	synonymous_variant	Exon 3 of 8		NP_001121186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
HIVEP3	ENST00000372583.6 link	c.3657G>A	p.Gln1219Gln	synonymous_variant	Exon 4 of 9	1	NM_024503.5	ENSP00000361664.1
HIVEP3	ENST00000372584.5 link	c.3657G>A	p.Gln1219Gln	synonymous_variant	Exon 3 of 8	1		ENSP00000361665.1
HIVEP3	ENST00000643665.1 link	c.3657G>A	p.Gln1219Gln	synonymous_variant	Exon 3 of 8			ENSP00000494598.1

Frequencies

GnomAD3 genomes

AF:

0.980

AC:

148874

AN:

151906

Hom.:

73015

Cov.:

show subpopulations

Gnomad AFR

AF:

0.931

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.992

Gnomad ASJ

AF:

1.00

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

1.00

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.997

Gnomad NFE

AF:

1.00

Gnomad OTH

AF:

0.985

GnomAD2 exomes

AF:

0.994

AC:

199882

AN:

201080

AF XY:

0.995

show subpopulations

Gnomad AFR exome

AF:

0.931

Gnomad AMR exome

AF:

0.997

Gnomad ASJ exome

AF:

1.00

Gnomad EAS exome

AF:

1.00

Gnomad FIN exome

AF:

1.00

Gnomad NFE exome

AF:

1.00

Gnomad OTH exome

AF:

0.997

GnomAD4 exome

AF:

0.998

AC:

1393219

AN:

1396130

Hom.:

695259

Cov.:

AF XY:

0.998

AC XY:

685202

AN XY:

686448

show subpopulations

African (AFR)

AF:

0.923

AC:

29308

AN:

31736

American (AMR)

AF:

0.996

AC:

36880

AN:

37010

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

21574

AN:

21574

East Asian (EAS)

AF:

1.00

AC:

39096

AN:

39096

South Asian (SAS)

AF:

1.00

AC:

74921

AN:

74928

European-Finnish (FIN)

AF:

1.00

AC:

50296

AN:

50296

Middle Eastern (MID)

AF:

0.996

AC:

5403

AN:

5426

European-Non Finnish (NFE)

AF:

1.00

AC:

1078430

AN:

1078506

Other (OTH)

AF:

0.996

AC:

57311

AN:

57558

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

162

325

487

650

812

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21568

43136

64704

86272

107840

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.980

AC:

148977

AN:

152024

Hom.:

73060

Cov.:

AF XY:

0.980

AC XY:

72816

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.931

AC:

38533

AN:

41408

American (AMR)

AF:

0.992

AC:

15173

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

3472

AN:

3472

East Asian (EAS)

AF:

1.00

AC:

5157

AN:

5158

South Asian (SAS)

AF:

1.00

AC:

4799

AN:

4800

European-Finnish (FIN)

AF:

1.00

AC:

10599

AN:

10600

Middle Eastern (MID)

AF:

0.997

AC:

293

AN:

294

European-Non Finnish (NFE)

AF:

1.00

AC:

67965

AN:

67984

Other (OTH)

AF:

0.985

AC:

2074

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

146

291

437

582

728

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

912

1824

2736

3648

4560

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.985

Hom.:

21666

Bravo

AF:

0.977

Asia WGS

AF:

0.994

AC:

3456

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

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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 -

HIVEP3-related disorder

Benign:1

Mar 23, 2022

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

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

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

0.48

(source)

DANN

Benign

0.36

PhyloP100

0.39

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over