Genetic Variant HIVEP3:c.5208-17940C>A (chr1-41542850-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024503.5(HIVEP3):c.5208-17940C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 155,202 control chromosomes in the GnomAD database, including 3,434 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.19 ( 3338 hom., cov: 32)

Exomes 𝑓: 0.23 ( 96 hom. )

Consequence

HIVEP3
NM_024503.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0350

Publications

4 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:

ENSG00000230638 (HGNC:):

ENSG00000230638 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
HIVEP3	NM_024503.5 link	c.5208-17940C>A	intron_variant	Intron 5 of 8	ENST00000372583.6	NP_078779.2	Q5T1R4-1
LOC100418723		n.41542850G>T	intragenic_variant
HIVEP3	NM_001127714.3 link	c.5208-17940C>A	intron_variant	Intron 4 of 7		NP_001121186.1	Q5T1R4-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HIVEP3	ENST00000372583.6 link	c.5208-17940C>A		intron_variant	Intron 5 of 8	1	NM_024503.5	ENSP00000361664.1		Q5T1R4-1

Frequencies

GnomAD3 genomes

AF:

0.188

AC:

28518

AN:

152080

Hom.:

3337

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0565

Gnomad AMI

AF:

0.373

Gnomad AMR

AF:

0.150

Gnomad ASJ

AF:

0.192

Gnomad EAS

AF:

0.0495

Gnomad SAS

AF:

0.187

Gnomad FIN

AF:

0.250

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.274

Gnomad OTH

AF:

0.182

GnomAD4 exome

AF:

0.235

AC:

705

AN:

3004

Hom.:

Cov.:

AF XY:

0.245

AC XY:

449

AN XY:

1836

show subpopulations

African (AFR)

AF:

0.0893

AC:

AN:

American (AMR)

AF:

0.0919

AC:

AN:

446

Ashkenazi Jewish (ASJ)

AF:

0.288

AC:

AN:

East Asian (EAS)

AF:

0.0538

AC:

AN:

130

South Asian (SAS)

AF:

0.208

AC:

AN:

144

European-Finnish (FIN)

AF:

0.328

AC:

AN:

262

Middle Eastern (MID)

AF:

0.133

AC:

AN:

158

European-Non Finnish (NFE)

AF:

0.288

AC:

460

AN:

1596

Other (OTH)

AF:

0.250

AC:

AN:

160

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

109

136

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.187

AC:

28505

AN:

152198

Hom.:

3338

Cov.:

AF XY:

0.184

AC XY:

13683

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.0563

AC:

2339

AN:

41548

American (AMR)

AF:

0.150

AC:

2290

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.192

AC:

667

AN:

3472

East Asian (EAS)

AF:

0.0496

AC:

257

AN:

5184

South Asian (SAS)

AF:

0.187

AC:

902

AN:

4822

European-Finnish (FIN)

AF:

0.250

AC:

2643

AN:

10582

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.274

AC:

18644

AN:

67984

Other (OTH)

AF:

0.179

AC:

379

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1128

2256

3384

4512

5640

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

312

624

936

1248

1560

<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:

0.237

Hom.:

5819

Bravo

AF:

0.173

Asia WGS

AF:

0.139

AC:

486

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

2.4

(source)

DANN

Benign

0.60

PhyloP100

-0.035

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over