Variant 1-41510649-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_024503.5(HIVEP3):c.7023C>T(p.Pro2341=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00401 in 1,537,602 control chromosomes in the GnomAD database, including 183 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0066 ( 22 hom., cov: 33)

Exomes 𝑓: 0.0037 ( 161 hom. )

Consequence

HIVEP3
NM_024503.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0380

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 made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 1-41510649-G-A is Benign according to our data. Variant chr1-41510649-G-A is described in ClinVar as [Benign]. Clinvar id is 3060063.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HIVEP3	NM_024503.5 linkuse as main transcript	c.7023C>T	p.Pro2341=	synonymous_variant	9/9	ENST00000372583.6
HIVEP3	NM_001127714.3 linkuse as main transcript	c.7020C>T	p.Pro2340=	synonymous_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HIVEP3	ENST00000372583.6 linkuse as main transcript	c.7023C>T	p.Pro2341=	synonymous_variant	9/9	1	NM_024503.5	P5	Q5T1R4-1
HIVEP3	ENST00000372584.5 linkuse as main transcript	c.7020C>T	p.Pro2340=	synonymous_variant	8/8	1		A2	Q5T1R4-2
HIVEP3	ENST00000643665.1 linkuse as main transcript	c.7020C>T	p.Pro2340=	synonymous_variant	8/8			A2	Q5T1R4-2
HIVEP3	ENST00000460604.1 linkuse as main transcript	n.1950C>T		non_coding_transcript_exon_variant	5/5	2

Frequencies

GnomAD3 genomes

AF:

0.00662

AC:

1007

AN:

152196

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00512

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0160

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.0851

Gnomad SAS

AF:

0.00497

Gnomad FIN

AF:

0.00245

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000706

Gnomad OTH

AF:

0.00334

GnomAD3 exomes

AF:

0.0131

AC:

1854

AN:

141532

Hom.:

AF XY:

0.0119

AC XY:

900

AN XY:

75946

show subpopulations

Gnomad AFR exome

AF:

0.00472

Gnomad AMR exome

AF:

0.0287

Gnomad ASJ exome

AF:

0.000645

Gnomad EAS exome

AF:

0.0853

Gnomad SAS exome

AF:

0.00415

Gnomad FIN exome

AF:

0.00195

Gnomad NFE exome

AF:

0.000666

Gnomad OTH exome

AF:

0.00690

GnomAD4 exome

AF:

0.00373

AC:

5168

AN:

1385288

Hom.:

161

Cov.:

AF XY:

0.00368

AC XY:

2510

AN XY:

681694

show subpopulations

Gnomad4 AFR exome

AF:

0.00519

Gnomad4 AMR exome

AF:

0.0263

Gnomad4 ASJ exome

AF:

0.000567

Gnomad4 EAS exome

AF:

0.0818

Gnomad4 SAS exome

AF:

0.00445

Gnomad4 FIN exome

AF:

0.00192

Gnomad4 NFE exome

AF:

0.000405

Gnomad4 OTH exome

AF:

0.00489

GnomAD4 genome

AF:

0.00659

AC:

1003

AN:

152314

Hom.:

Cov.:

AF XY:

0.00771

AC XY:

574

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.00513

Gnomad4 AMR

AF:

0.0159

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.0847

Gnomad4 SAS

AF:

0.00498

Gnomad4 FIN

AF:

0.00245

Gnomad4 NFE

AF:

0.000706

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00166

Hom.:

Bravo

AF:

0.00806

Asia WGS

AF:

0.0320

AC:

112

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

HIVEP3-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 08, 2020

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). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

Cadd

Benign

0.50

Dann

Benign

0.63

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over