dbSNP rs661225: HIVEP3:c.-801+73919C>T (chr1-41844494-G-A) – 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.-801+73919C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 152,056 control chromosomes in the GnomAD database, including 30,903 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 0.62 ( 30903 hom., cov: 32)

Consequence

HIVEP3
NM_024503.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.493

Publications

5 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:

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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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HIVEP3	NM_024503.5	MANE Select	c.-801+73919C>T		intron	N/A	NP_078779.2	Q5T1R4-1
	HIVEP3	NM_001127714.3		c.-721+73919C>T		intron	N/A	NP_001121186.1	Q5T1R4-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HIVEP3	ENST00000372583.6	TSL:1 MANE Select	c.-801+73919C>T		intron	N/A	ENSP00000361664.1	Q5T1R4-1
	HIVEP3	ENST00000372584.5	TSL:1	c.-721+73919C>T		intron	N/A	ENSP00000361665.1	Q5T1R4-2

Frequencies

GnomAD3 genomes

AF:

0.622

AC:

94569

AN:

151938

Hom.:

30870

Cov.:

show subpopulations

Gnomad AFR

AF:

0.807

Gnomad AMI

AF:

0.467

Gnomad AMR

AF:

0.559

Gnomad ASJ

AF:

0.612

Gnomad EAS

AF:

0.193

Gnomad SAS

AF:

0.438

Gnomad FIN

AF:

0.566

Gnomad MID

AF:

0.560

Gnomad NFE

AF:

0.581

Gnomad OTH

AF:

0.626

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.623

AC:

94661

AN:

152056

Hom.:

30903

Cov.:

AF XY:

0.613

AC XY:

45583

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.807

AC:

33486

AN:

41482

American (AMR)

AF:

0.560

AC:

8540

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.612

AC:

2125

AN:

3470

East Asian (EAS)

AF:

0.193

AC:

996

AN:

5170

South Asian (SAS)

AF:

0.440

AC:

2118

AN:

4818

European-Finnish (FIN)

AF:

0.566

AC:

5979

AN:

10568

Middle Eastern (MID)

AF:

0.565

AC:

166

AN:

294

European-Non Finnish (NFE)

AF:

0.581

AC:

39517

AN:

67972

Other (OTH)

AF:

0.619

AC:

1309

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1711

3421

5132

6842

8553

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

754

1508

2262

3016

3770

<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:

0.606

Hom.:

4982

Bravo

AF:

0.632

Asia WGS

AF:

0.354

AC:

1234

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

6.0

(source)

DANN

Benign

0.75

PhyloP100

0.49

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over