Genetic Variant NM_024503.5:c.5208-17940C>A (chr1-41542850-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . 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:

LOC100418723 (HGNC:):

LOC100418723 links:

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new If you want to explore the variant's impact on the transcript NM_024503.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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.

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.5208-17940C>A		intron	N/A	NP_078779.2	Q5T1R4-1
	HIVEP3	NM_001127714.3		c.5208-17940C>A		intron	N/A	NP_001121186.1	Q5T1R4-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
HIVEP3	ENST00000372583.6	TSL:1 MANE Select	c.5208-17940C>A	intron	N/A	ENSP00000361664.1	Q5T1R4-1
HIVEP3	ENST00000372584.5	TSL:1	c.5208-17940C>A	intron	N/A	ENSP00000361665.1	Q5T1R4-2
HIVEP3	ENST00000643665.1		c.5208-17940C>A	intron	N/A	ENSP00000494598.1	Q5T1R4-2

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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

Computational scores

Splicing

Publications

Other links and lift over