1-41513485-A-G

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.5736T>C(p.Ala1912Ala) 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 (★★).

Frequency

Genomes: 𝑓 0.65 ( 32343 hom., cov: 31)

Exomes 𝑓: 0.63 ( 296150 hom. )

Consequence

HIVEP3
NM_024503.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.830

Publications

16 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:

ENSG00000295052 (HGNC:):

ENSG00000295052 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=-0.85).

BP6

Variant 1-41513485-A-G is Benign according to our data. Variant chr1-41513485-A-G is described in ClinVar as Benign. ClinVar VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024503.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HIVEP3	NM_024503.5	MANE Select	c.5736T>C	p.Ala1912Ala	synonymous	Exon 8 of 9	NP_078779.2
	HIVEP3	NM_001127714.3		c.5736T>C	p.Ala1912Ala	synonymous	Exon 7 of 8	NP_001121186.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
HIVEP3	ENST00000372583.6	TSL:1 MANE Select	c.5736T>C	p.Ala1912Ala	synonymous	Exon 8 of 9	ENSP00000361664.1
HIVEP3	ENST00000372584.5	TSL:1	c.5736T>C	p.Ala1912Ala	synonymous	Exon 7 of 8	ENSP00000361665.1
HIVEP3	ENST00000643665.1		c.5736T>C	p.Ala1912Ala	synonymous	Exon 7 of 8	ENSP00000494598.1

Frequencies

GnomAD3 genomes

AF:

0.648

AC:

98349

AN:

151752

Hom.:

32315

Cov.:

show subpopulations

Gnomad AFR

AF:

0.652

Gnomad AMI

AF:

0.795

Gnomad AMR

AF:

0.682

Gnomad ASJ

AF:

0.618

Gnomad EAS

AF:

0.990

Gnomad SAS

AF:

0.713

Gnomad FIN

AF:

0.664

Gnomad MID

AF:

0.642

Gnomad NFE

AF:

0.606

Gnomad OTH

AF:

0.618

GnomAD2 exomes

AF:

0.670

AC:

163045

AN:

243254

AF XY:

0.665

show subpopulations

Gnomad AFR exome

AF:

0.656

Gnomad AMR exome

AF:

0.719

Gnomad ASJ exome

AF:

0.643

Gnomad EAS exome

AF:

0.996

Gnomad FIN exome

AF:

0.660

Gnomad NFE exome

AF:

0.602

Gnomad OTH exome

AF:

0.638

GnomAD4 exome

AF:

0.633

AC:

922403

AN:

1456668

Hom.:

296150

Cov.:

AF XY:

0.634

AC XY:

459276

AN XY:

724360

show subpopulations

African (AFR)

AF:

0.650

AC:

21721

AN:

33426

American (AMR)

AF:

0.711

AC:

31620

AN:

44466

Ashkenazi Jewish (ASJ)

AF:

0.637

AC:

16592

AN:

26032

East Asian (EAS)

AF:

0.992

AC:

39320

AN:

39644

South Asian (SAS)

AF:

0.689

AC:

59298

AN:

86060

European-Finnish (FIN)

AF:

0.658

AC:

33489

AN:

50910

Middle Eastern (MID)

AF:

0.624

AC:

3519

AN:

5640

European-Non Finnish (NFE)

AF:

0.610

AC:

677487

AN:

1110266

Other (OTH)

AF:

0.654

AC:

39357

AN:

60224

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

20452

40904

61356

81808

102260

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18506

37012

55518

74024

92530

<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:

0.648

AC:

98428

AN:

151870

Hom.:

32343

Cov.:

AF XY:

0.654

AC XY:

48493

AN XY:

74202

show subpopulations

African (AFR)

AF:

0.653

AC:

27026

AN:

41412

American (AMR)

AF:

0.682

AC:

10433

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.618

AC:

2145

AN:

3472

East Asian (EAS)

AF:

0.990

AC:

5076

AN:

5128

South Asian (SAS)

AF:

0.712

AC:

3422

AN:

4808

European-Finnish (FIN)

AF:

0.664

AC:

7005

AN:

10554

Middle Eastern (MID)

AF:

0.646

AC:

190

AN:

294

European-Non Finnish (NFE)

AF:

0.605

AC:

41109

AN:

67896

Other (OTH)

AF:

0.616

AC:

1299

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1760

3520

5280

7040

8800

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

798

1596

2394

3192

3990

<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:

0.613

Hom.:

12827

Bravo

AF:

0.649

Asia WGS

AF:

0.806

AC:

2803

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: Frequency

HIVEP3-related disorder

Benign:1

Oct 17, 2019

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.7

(source)

DANN

Benign

0.37

PhyloP100

0.83

Mutation Taster

=100/0

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over