chr1-41583361-G-A

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.1437C>T(p.Ser479Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.992 in 1,612,766 control chromosomes in the GnomAD database, including 794,395 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.96 ( 70096 hom., cov: 29)

Exomes 𝑓: 1.0 ( 724299 hom. )

Consequence

HIVEP3
NM_024503.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.366

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=-0.54).

BP6

Variant 1-41583361-G-A is Benign according to our data. Variant chr1-41583361-G-A is described in ClinVar as Benign. ClinVar VariationId is 402946.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.366 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.1437C>T	p.Ser479Ser	synonymous_variant	Exon 4 of 9	ENST00000372583.6	NP_078779.2
HIVEP3	NM_001127714.3 link	c.1437C>T	p.Ser479Ser	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.1437C>T	p.Ser479Ser	synonymous_variant	Exon 4 of 9	1	NM_024503.5	ENSP00000361664.1
HIVEP3	ENST00000372584.5 link	c.1437C>T	p.Ser479Ser	synonymous_variant	Exon 3 of 8	1		ENSP00000361665.1
HIVEP3	ENST00000643665.1 link	c.1437C>T	p.Ser479Ser	synonymous_variant	Exon 3 of 8			ENSP00000494598.1

Frequencies

GnomAD3 genomes

AF:

0.958

AC:

145593

AN:

152026

Hom.:

70054

Cov.:

show subpopulations

Gnomad AFR

AF:

0.852

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.986

Gnomad ASJ

AF:

1.00

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.999

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.997

Gnomad NFE

AF:

1.00

Gnomad OTH

AF:

0.968

GnomAD2 exomes

AF:

0.989

AC:

247800

AN:

250492

AF XY:

0.992

show subpopulations

Gnomad AFR exome

AF:

0.852

Gnomad AMR exome

AF:

0.994

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:

0.996

GnomAD4 exome

AF:

0.996

AC:

1454167

AN:

1460622

Hom.:

724299

Cov.:

AF XY:

0.996

AC XY:

723665

AN XY:

726454

show subpopulations

African (AFR)

AF:

0.842

AC:

28173

AN:

33468

American (AMR)

AF:

0.993

AC:

44319

AN:

44648

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

26068

AN:

26068

East Asian (EAS)

AF:

1.00

AC:

39672

AN:

39672

South Asian (SAS)

AF:

1.00

AC:

86025

AN:

86046

European-Finnish (FIN)

AF:

1.00

AC:

53366

AN:

53366

Middle Eastern (MID)

AF:

0.992

AC:

5717

AN:

5766

European-Non Finnish (NFE)

AF:

1.00

AC:

1111079

AN:

1111262

Other (OTH)

AF:

0.990

AC:

59748

AN:

60326

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

340

680

1020

1360

1700

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21662

43324

64986

86648

108310

<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:

0.958

AC:

145692

AN:

152144

Hom.:

70096

Cov.:

AF XY:

0.958

AC XY:

71267

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.852

AC:

35343

AN:

41484

American (AMR)

AF:

0.986

AC:

15089

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

3472

AN:

3472

East Asian (EAS)

AF:

1.00

AC:

5120

AN:

5120

South Asian (SAS)

AF:

0.999

AC:

4811

AN:

4814

European-Finnish (FIN)

AF:

1.00

AC:

10614

AN:

10614

Middle Eastern (MID)

AF:

0.997

AC:

293

AN:

294

European-Non Finnish (NFE)

AF:

1.00

AC:

67996

AN:

68026

Other (OTH)

AF:

0.969

AC:

2042

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

281

562

844

1125

1406

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:

0.984

Hom.:

116462

Bravo

AF:

0.952

Asia WGS

AF:

0.990

AC:

3442

AN:

3478

EpiCase

AF:

1.00

EpiControl

AF:

1.00

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 28, 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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

1.5

(source)

DANN

Benign

0.82

PhyloP100

0.37

Mutation Taster

=98/2

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over