rs1007221

Variant names:

• chr1-41574100-C-T
• rs1007221
• NM_024503.5:c.5207+1444G>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.5207+1444G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,010 control chromosomes in the GnomAD database, including 3,777 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 0.20 (3777 hom., cov: 31)
• Consequence: HIVEP3 NM_024503.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 1 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 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.5207+1444G>A		intron	N/A	NP_078779.2
	HIVEP3	NM_001127714.3		c.5207+1444G>A		intron	N/A	NP_001121186.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HIVEP3	ENST00000372583.6	TSL:1 MANE Select	c.5207+1444G>A		intron	N/A	ENSP00000361664.1
	HIVEP3	ENST00000372584.5	TSL:1	c.5207+1444G>A		intron	N/A	ENSP00000361665.1
	HIVEP3	ENST00000643665.1		c.5207+1444G>A		intron	N/A	ENSP00000494598.1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30077 AN: 151892 Hom.: 3772 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.198 AC: 30109 AN: 152010 Hom.: 3777 Cov.: 31 AF XY: 0.204 AC XY: 15131 AN XY: 74298

African (AFR) AF: 0.277 AC: 11502 AN: 41456

American (AMR) AF: 0.321 AC: 4901 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 596 AN: 3468

East Asian (EAS) AF: 0.448 AC: 2305 AN: 5150

South Asian (SAS) AF: 0.206 AC: 990 AN: 4798

European-Finnish (FIN) AF: 0.150 AC: 1588 AN: 10586

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.113 AC: 7665 AN: 67960

Other (OTH) AF: 0.213 AC: 448 AN: 2108

Alfa AF: 0.167 Hom.: 1114

Bravo AF: 0.214

Asia WGS AF: 0.311 AC: 1085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.37
PhyloP100		0.32
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: rs1007221; hg19: chr1-42039771;