1-41510659-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_024503.5(HIVEP3):c.7013C>T(p.Pro2338Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00504 in 1,526,972 control chromosomes in the GnomAD database, including 330 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. P2338P) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.026 (183 hom., cov: 33)
  • Exomes 𝑓: 0.0027 (147 hom.)
• Consequence: HIVEP3 NM_024503.5 missense
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.188

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0024409592).
• BP6: Variant 1-41510659-G-A is Benign according to our data. Variant chr1-41510659-G-A is described in ClinVar as [Benign]. Clinvar id is 3037301.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HIVEP3	NM_024503.5	c.7013C>T	p.Pro2338Leu	missense_variant	9/9	ENST00000372583.6
HIVEP3	NM_001127714.3	c.7010C>T	p.Pro2337Leu	missense_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HIVEP3	ENST00000372583.6	c.7013C>T	p.Pro2338Leu	missense_variant	9/9	1	NM_024503.5	P5
HIVEP3	ENST00000372584.5	c.7010C>T	p.Pro2337Leu	missense_variant	8/8	1		A2
HIVEP3	ENST00000643665.1	c.7010C>T	p.Pro2337Leu	missense_variant	8/8			A2
HIVEP3	ENST00000460604.1	n.1940C>T		non_coding_transcript_exon_variant	5/5	2

Frequencies

GnomAD3 genomes AF: 0.0260 AC: 3956 AN: 152162 Hom.: 183 Cov.: 33

Gnomad AFR AF: 0.0904

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00929

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000250

Gnomad OTH AF: 0.0234

GnomAD3 exomes AF: 0.00618 AC: 834 AN: 135002 Hom.: 28 AF XY: 0.00505 AC XY: 366 AN XY: 72510

Gnomad AFR exome AF: 0.102

Gnomad AMR exome AF: 0.00290

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000366

Gnomad SAS exome AF: 0.000623

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000318

Gnomad OTH exome AF: 0.00205

GnomAD4 exome AF: 0.00272 AC: 3737 AN: 1374692 Hom.: 147 Cov.: 34 AF XY: 0.00238 AC XY: 1608 AN XY: 675394

Gnomad4 AFR exome AF: 0.0958

Gnomad4 AMR exome AF: 0.00384

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000197

Gnomad4 SAS exome AF: 0.000710

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000223

Gnomad4 OTH exome AF: 0.00543

GnomAD4 genome AF: 0.0260 AC: 3961 AN: 152280 Hom.: 183 Cov.: 33 AF XY: 0.0257 AC XY: 1914 AN XY: 74470

Gnomad4 AFR AF: 0.0902

Gnomad4 AMR AF: 0.00928

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000250

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.00274 Hom.: 4

Bravo AF: 0.0300

ESP6500AA AF: 0.0679 AC: 273

ESP6500EA AF: 0.000644 AC: 5

ExAC AF: 0.00638 AC: 664

Asia WGS AF: 0.00346 AC: 12 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

HIVEP3-related disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 23, 2019

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
AlphaMissense	Benign	0.057
BayesDel_addAF	Benign	-0.80	T
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.020
Dann	Benign	0.42
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.0046	N
MetaRNN	Benign	0.0024	T;T;T
MetaSVM	Benign	-0.92	T
MutationTaster	Benign	1.0	N;N;N;N
PrimateAI	Benign	0.31	T
Polyphen		0.0	B;B;B
Vest4		0.032, 0.043
MVP		0.055
MPC		0.19
ClinPred		0.0014	T
GERP RS		-5.5
Varity_R		0.025
gMVP		0.028

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

Other links and lift over

dbSNP: rs58930436; hg19: chr1-41976330;