Variant chr1-41510657-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_024503.5(HIVEP3):c.7015A>T(p.Thr2339Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T2339A) has been classified as Benign.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

HIVEP3
NM_024503.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.588

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:

HIVEP3 (HGNC:):

HIVEP3 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.066645116).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HIVEP3	NM_024503.5 linkuse as main transcript	c.7015A>T	p.Thr2339Ser	missense_variant	9/9	ENST00000372583.6	NP_078779.2	Q5T1R4-1
HIVEP3	NM_001127714.3 linkuse as main transcript	c.7012A>T	p.Thr2338Ser	missense_variant	8/8		NP_001121186.1	Q5T1R4-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
HIVEP3	ENST00000372583.6 linkuse as main transcript	c.7015A>T	p.Thr2339Ser	missense_variant	9/9	1	NM_024503.5	ENSP00000361664.1	Q5T1R4-1
HIVEP3	ENST00000372584.5 linkuse as main transcript	c.7012A>T	p.Thr2338Ser	missense_variant	8/8	1		ENSP00000361665.1	Q5T1R4-2
HIVEP3	ENST00000643665.1 linkuse as main transcript	c.7012A>T	p.Thr2338Ser	missense_variant	8/8			ENSP00000494598.1	Q5T1R4-2
HIVEP3	ENST00000460604.1 linkuse as main transcript	n.1942A>T		non_coding_transcript_exon_variant	5/5	2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1381538

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

679736

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.067

BayesDel_addAF

Benign

-0.40

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.9

DANN

Benign

0.36

DEOGEN2

Benign

0.071

.;T;.

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.059

LIST_S2

Benign

0.24

.;T;T

M_CAP

Benign

0.0067

MetaRNN

Benign

0.067

T;T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

0.34

.;N;.

PrimateAI

Benign

0.38

PROVEAN

Benign

0.13

.;N;N

REVEL

Benign

0.049

Sift

Benign

0.052

.;T;T

Sift4G

Benign

0.25

.;T;T

Polyphen

0.034

B;B;B

Vest4

0.045, 0.040

MutPred

0.096

.;Gain of glycosylation at P2338 (P = 0.1636);.;

MVP

0.061

MPC

0.17

ClinPred

0.061

GERP RS

2.2

Varity_R

0.042

gMVP

0.034

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over