chr1-41629048-A-G

Variant summary

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

The NM_024503.5(HIVEP3):​c.-720-101T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 844,954 control chromosomes in the GnomAD database, including 112,683 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 0.46 ( 16834 hom., cov: 32)
Exomes 𝑓: 0.52 ( 95849 hom. )

Consequence

HIVEP3
NM_024503.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.54

Publications

2 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]

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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HIVEP3NM_024503.5 linkc.-720-101T>C intron_variant Intron 2 of 8 ENST00000372583.6 NP_078779.2 Q5T1R4-1
HIVEP3NM_001127714.3 linkc.-720-101T>C intron_variant Intron 1 of 7 NP_001121186.1 Q5T1R4-2
LOC128125817NM_001415000.1 linkc.-232T>C upstream_gene_variant NP_001401929.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HIVEP3ENST00000372583.6 linkc.-720-101T>C intron_variant Intron 2 of 8 1 NM_024503.5 ENSP00000361664.1 Q5T1R4-1
HIVEP3ENST00000372584.5 linkc.-720-101T>C intron_variant Intron 1 of 7 1 ENSP00000361665.1 Q5T1R4-2
HIVEP3ENST00000643665.1 linkc.-720-101T>C intron_variant Intron 1 of 7 ENSP00000494598.1 Q5T1R4-2
ENSG00000284895ENST00000646142.1 linkc.-232T>C upstream_gene_variant ENSP00000494286.1 A0A2R8Y556

Frequencies

GnomAD3 genomes
AF:
0.462
AC:
70205
AN:
151958
Hom.:
16837
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.363
Gnomad AMI
AF:
0.730
Gnomad AMR
AF:
0.373
Gnomad ASJ
AF:
0.540
Gnomad EAS
AF:
0.407
Gnomad SAS
AF:
0.427
Gnomad FIN
AF:
0.501
Gnomad MID
AF:
0.430
Gnomad NFE
AF:
0.536
Gnomad OTH
AF:
0.438
GnomAD4 exome
AF:
0.523
AC:
362292
AN:
692878
Hom.:
95849
AF XY:
0.522
AC XY:
174301
AN XY:
333698
show subpopulations
African (AFR)
AF:
0.353
AC:
5332
AN:
15110
American (AMR)
AF:
0.327
AC:
2278
AN:
6972
Ashkenazi Jewish (ASJ)
AF:
0.537
AC:
6136
AN:
11428
East Asian (EAS)
AF:
0.332
AC:
7508
AN:
22622
South Asian (SAS)
AF:
0.429
AC:
4837
AN:
11280
European-Finnish (FIN)
AF:
0.489
AC:
8822
AN:
18038
Middle Eastern (MID)
AF:
0.473
AC:
980
AN:
2074
European-Non Finnish (NFE)
AF:
0.541
AC:
311127
AN:
575238
Other (OTH)
AF:
0.507
AC:
15272
AN:
30116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
7975
15950
23925
31900
39875
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
9400
18800
28200
37600
47000
<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:
0.462
AC:
70222
AN:
152076
Hom.:
16834
Cov.:
32
AF XY:
0.457
AC XY:
33950
AN XY:
74336
show subpopulations
African (AFR)
AF:
0.363
AC:
15056
AN:
41468
American (AMR)
AF:
0.373
AC:
5704
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
0.540
AC:
1872
AN:
3468
East Asian (EAS)
AF:
0.408
AC:
2114
AN:
5180
South Asian (SAS)
AF:
0.427
AC:
2058
AN:
4824
European-Finnish (FIN)
AF:
0.501
AC:
5300
AN:
10572
Middle Eastern (MID)
AF:
0.429
AC:
126
AN:
294
European-Non Finnish (NFE)
AF:
0.536
AC:
36405
AN:
67954
Other (OTH)
AF:
0.436
AC:
921
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1922
3844
5767
7689
9611
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
650
1300
1950
2600
3250
<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:
0.489
Hom.:
2292
Bravo
AF:
0.449
Asia WGS
AF:
0.401
AC:
1398
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.080
DANN
Benign
0.51
PhyloP100
-1.5
PromoterAI
0.010
Neutral
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs2038978; hg19: chr1-42094719; API