Variant 6-142753563-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_006734.4(HIVEP2):c.6885A>G(p.Pro2295=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 1,613,816 control chromosomes in the GnomAD database, including 355,760 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.71 ( 38756 hom., cov: 32)

Exomes 𝑓: 0.66 ( 317004 hom. )

Consequence

HIVEP2
NM_006734.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.141

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:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 6-142753563-T-C is Benign according to our data. Variant chr6-142753563-T-C is described in ClinVar as [Benign]. Clinvar id is 402939.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-142753563-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.141 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HIVEP2	NM_006734.4 linkuse as main transcript	c.6885A>G	p.Pro2295=	synonymous_variant	10/10	ENST00000367603.8	NP_006725.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HIVEP2	ENST00000367603.8 linkuse as main transcript	c.6885A>G	p.Pro2295=	synonymous_variant	10/10	1	NM_006734.4	ENSP00000356575	P1
	ENST00000437067.1 linkuse as main transcript	n.153T>C		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes

AF:

0.708

AC:

107554

AN:

151974

Hom.:

38716

Cov.:

show subpopulations

Gnomad AFR

AF:

0.838

Gnomad AMI

AF:

0.805

Gnomad AMR

AF:

0.669

Gnomad ASJ

AF:

0.702

Gnomad EAS

AF:

0.831

Gnomad SAS

AF:

0.756

Gnomad FIN

AF:

0.648

Gnomad MID

AF:

0.655

Gnomad NFE

AF:

0.633

Gnomad OTH

AF:

0.703

GnomAD3 exomes

AF:

0.686

AC:

170775

AN:

249086

Hom.:

59272

AF XY:

0.684

AC XY:

92442

AN XY:

135158

show subpopulations

Gnomad AFR exome

AF:

0.841

Gnomad AMR exome

AF:

0.679

Gnomad ASJ exome

AF:

0.696

Gnomad EAS exome

AF:

0.841

Gnomad SAS exome

AF:

0.754

Gnomad FIN exome

AF:

0.640

Gnomad NFE exome

AF:

0.633

Gnomad OTH exome

AF:

0.652

GnomAD4 exome

AF:

0.656

AC:

959160

AN:

1461724

Hom.:

317004

Cov.:

AF XY:

0.659

AC XY:

478866

AN XY:

727178

show subpopulations

Gnomad4 AFR exome

AF:

0.848

Gnomad4 AMR exome

AF:

0.681

Gnomad4 ASJ exome

AF:

0.700

Gnomad4 EAS exome

AF:

0.836

Gnomad4 SAS exome

AF:

0.754

Gnomad4 FIN exome

AF:

0.634

Gnomad4 NFE exome

AF:

0.634

Gnomad4 OTH exome

AF:

0.675

GnomAD4 genome

AF:

0.708

AC:

107647

AN:

152092

Hom.:

38756

Cov.:

AF XY:

0.708

AC XY:

52630

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.838

Gnomad4 AMR

AF:

0.669

Gnomad4 ASJ

AF:

0.702

Gnomad4 EAS

AF:

0.831

Gnomad4 SAS

AF:

0.757

Gnomad4 FIN

AF:

0.648

Gnomad4 NFE

AF:

0.633

Gnomad4 OTH

AF:

0.704

Alfa

AF:

0.651

Hom.:

64920

Bravo

AF:

0.714

Asia WGS

AF:

0.773

AC:

2688

AN:

3478

EpiCase

AF:

0.636

EpiControl

AF:

0.628

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 17, 2019	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Intellectual disability, autosomal dominant 43

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.61

DANN

Benign

0.37

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