rs10493102

Variant names:

• chr1-41542850-G-T
• rs10493102
• NM_024503.5:c.5208-17940C>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.5208-17940C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 155,202 control chromosomes in the GnomAD database, including 3,434 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 0.19 (3338 hom., cov: 32)
  • Exomes 𝑓: 0.23 (96 hom.)
• Consequence: HIVEP3 NM_024503.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

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]

ENSG00000230638 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HIVEP3	NM_024503.5	c.5208-17940C>A		intron_variant	Intron 5 of 8	ENST00000372583.6	NP_078779.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HIVEP3	ENST00000372583.6	c.5208-17940C>A		intron_variant	Intron 5 of 8	1	NM_024503.5	ENSP00000361664.1

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28518 AN: 152080 Hom.: 3337 Cov.: 32

Gnomad AFR AF: 0.0565

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0495

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.182

GnomAD4 exome AF: 0.235 AC: 705 AN: 3004 Hom.: 96 Cov.: 0 AF XY: 0.245 AC XY: 449 AN XY: 1836

Gnomad4 AFR exome AF: 0.0893 AC: 5 AN: 56

Gnomad4 AMR exome AF: 0.0919 AC: 41 AN: 446

Gnomad4 ASJ exome AF: 0.288 AC: 15 AN: 52

Gnomad4 EAS exome AF: 0.0538 AC: 7 AN: 130

Gnomad4 SAS exome AF: 0.208 AC: 30 AN: 144

Gnomad4 FIN exome AF: 0.328 AC: 86 AN: 262

Gnomad4 NFE exome AF: 0.288 AC: 460 AN: 1596

Gnomad4 Remaining exome AF: 0.250 AC: 40 AN: 160

GnomAD4 genome AF: 0.187 AC: 28505 AN: 152198 Hom.: 3338 Cov.: 32 AF XY: 0.184 AC XY: 13683 AN XY: 74408

Gnomad4 AFR AF: 0.0563 AC: 0.0562963 AN: 0.0562963

Gnomad4 AMR AF: 0.150 AC: 0.149791 AN: 0.149791

Gnomad4 ASJ AF: 0.192 AC: 0.192108 AN: 0.192108

Gnomad4 EAS AF: 0.0496 AC: 0.0495756 AN: 0.0495756

Gnomad4 SAS AF: 0.187 AC: 0.187059 AN: 0.187059

Gnomad4 FIN AF: 0.250 AC: 0.249764 AN: 0.249764

Gnomad4 NFE AF: 0.274 AC: 0.274241 AN: 0.274241

Gnomad4 OTH AF: 0.179 AC: 0.179281 AN: 0.179281

Alfa AF: 0.237 Hom.: 5819

Bravo AF: 0.173

Asia WGS AF: 0.139 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	2.4
DANN	Benign	0.60
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

Publications

LitVar

Other links and lift over

dbSNP: rs10493102; hg19: chr1-42008521;