rs117019703

Variant names:

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_006734.4(HIVEP2):c.7036C>T(p.Leu2346Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0037 in 1,613,938 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0027 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0038 ( 12 hom. )

Consequence

HIVEP2
NM_006734.4 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 6.08

Variant links:

Genes affected

HIVEP2 (HGNC:4921): (HIVEP zinc finger 2) This gene encodes a member of a family of closely related, large, zinc finger-containing transcription factors. The encoded protein regulates transcription by binding to regulatory regions of various cellular and viral genes that maybe involved in growth, development and metastasis. The protein contains the ZAS domain comprised of two widely separated regions of zinc finger motifs, a stretch of highly acidic amino acids and a serine/threonine-rich sequence. [provided by RefSeq, Nov 2012]

HIVEP2 links:

ENSG00000233138 (HGNC:):

ENSG00000233138 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.006490886).

BP6

Variant 6-142753412-G-A is Benign according to our data. Variant chr6-142753412-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 445845.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 405 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HIVEP2	NM_006734.4 link	c.7036C>T	p.Leu2346Phe	missense_variant	Exon 10 of 10	ENST00000367603.8	NP_006725.3	P31629

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HIVEP2	ENST00000367603.8 link	c.7036C>T	p.Leu2346Phe	missense_variant	Exon 10 of 10	1	NM_006734.4	ENSP00000356575.2		P31629

Frequencies

GnomAD3 genomes

AF:

0.00265

AC:

404

AN:

152190

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000627

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00131

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.00290

Gnomad FIN

AF:

0.00339

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00442

Gnomad OTH

AF:

0.000956

GnomAD3 exomes

AF:

0.00268

AC:

661

AN:

246880

Hom.:

AF XY:

0.00285

AC XY:

383

AN XY:

134228

show subpopulations

Gnomad AFR exome

AF:

0.00118

Gnomad AMR exome

AF:

0.00119

Gnomad ASJ exome

AF:

0.00191

Gnomad EAS exome

AF:

0.0000558

Gnomad SAS exome

AF:

0.00200

Gnomad FIN exome

AF:

0.00246

Gnomad NFE exome

AF:

0.00404

Gnomad OTH exome

AF:

0.00317

GnomAD4 exome

AF:

0.00380

AC:

5561

AN:

1461630

Hom.:

Cov.:

AF XY:

0.00374

AC XY:

2722

AN XY:

727104

show subpopulations

Gnomad4 AFR exome

AF:

0.000388

Gnomad4 AMR exome

AF:

0.00132

Gnomad4 ASJ exome

AF:

0.00199

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00212

Gnomad4 FIN exome

AF:

0.00209

Gnomad4 NFE exome

AF:

0.00449

Gnomad4 OTH exome

AF:

0.00237

GnomAD4 genome

AF:

0.00266

AC:

405

AN:

152308

Hom.:

Cov.:

AF XY:

0.00264

AC XY:

197

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.000626

Gnomad4 AMR

AF:

0.00131

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.000580

Gnomad4 SAS

AF:

0.00290

Gnomad4 FIN

AF:

0.00339

Gnomad4 NFE

AF:

0.00442

Gnomad4 OTH

AF:

0.000946

Alfa

AF:

0.00358

Hom.:

Bravo

AF:

0.00246

TwinsUK

AF:

0.00405

AC:

ALSPAC

AF:

0.00545

AC:

ESP6500AA

AF:

0.000507

AC:

ESP6500EA

AF:

0.00361

AC:

ExAC

AF:

0.00268

AC:

324

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00382

EpiControl

AF:

0.00290

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Jan 07, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 01, 2017

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Oct 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

HIVEP2: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.079

BayesDel_addAF

Benign

-0.45

BayesDel_noAF

Benign

-0.42

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.11

T;T;T

Eigen

Uncertain

0.47

Eigen_PC

Uncertain

0.54

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.87

.;.;D

M_CAP

Benign

0.0074

MetaRNN

Benign

0.0065

T;T;T

MetaSVM

Benign

-0.83

MutationAssessor

Uncertain

2.1

M;M;M

PrimateAI

Uncertain

0.50

PROVEAN

Benign

-0.63

N;N;N

REVEL

Benign

0.13

Sift

Benign

0.20

T;T;T

Sift4G

Benign

0.35

T;T;T

Polyphen

0.85

P;P;P

Vest4

0.19

MVP

0.068

MPC

0.53

ClinPred

0.019

GERP RS

5.8

Varity_R

0.047

gMVP

0.091

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