NM_024503.5:c.-522+1405G>A

Variant names:

• chr1-41627344-C-T
• rs752010
• NM_024503.5:c.-522+1405G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024503.5(HIVEP3):​c.-522+1405G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 152,046 control chromosomes in the GnomAD database, including 27,588 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (27588 hom., cov: 33)
• Consequence: HIVEP3 NM_024503.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364
• Publications: 10 publications found

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]

ENSG00000284895 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024503.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HIVEP3	NM_024503.5	MANE Select	c.-522+1405G>A		intron	N/A	NP_078779.2
	HIVEP3	NM_001127714.3		c.-522+1405G>A		intron	N/A	NP_001121186.1
	LOC128125817	NM_001415000.1		c.68+1405G>A		intron	N/A	NP_001401929.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HIVEP3	ENST00000372583.6	TSL:1 MANE Select	c.-522+1405G>A		intron	N/A	ENSP00000361664.1
	HIVEP3	ENST00000372584.5	TSL:1	c.-522+1405G>A		intron	N/A	ENSP00000361665.1
	ENSG00000284895	ENST00000646142.1		c.68+1405G>A		intron	N/A	ENSP00000494286.1

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89063 AN: 151928 Hom.: 27542 Cov.: 33

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.534

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.586 AC: 89165 AN: 152046 Hom.: 27588 Cov.: 33 AF XY: 0.579 AC XY: 43054 AN XY: 74326

African (AFR) AF: 0.790 AC: 32762 AN: 41486

American (AMR) AF: 0.415 AC: 6342 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1872 AN: 3468

East Asian (EAS) AF: 0.421 AC: 2173 AN: 5160

South Asian (SAS) AF: 0.468 AC: 2257 AN: 4822

European-Finnish (FIN) AF: 0.507 AC: 5355 AN: 10560

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36475 AN: 67948

Other (OTH) AF: 0.537 AC: 1130 AN: 2104

Alfa AF: 0.551 Hom.: 6910

Bravo AF: 0.588

Asia WGS AF: 0.483 AC: 1683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.46
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs752010; hg19: chr1-42093015;