rs2327514

Positions:

• chr6-12117322-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002114.4(HIVEP1):​c.95-2568G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0768 in 152,242 control chromosomes in the GnomAD database, including 646 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 0.077 (646 hom., cov: 32)
• Consequence: HIVEP1 NM_002114.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690

Genes affected

HIVEP1 (HGNC:4920): (HIVEP zinc finger 1) This gene encodes a transcription factor belonging to the ZAS family, members of which are large proteins that contain a ZAS domain - a modular protein structure consisting of a pair of C2H2 zinc fingers with an acidic-rich region and a serine/threonine-rich sequence. These proteins bind specifically to the DNA sequence motif, GGGACTTTCC, found in the enhancer elements of several viral promoters, including human immunodeficiency virus (HIV), and to related sequences found in the enhancer elements of a number of cellular promoters. This protein binds to this sequence motif, suggesting a role in the transcriptional regulation of both viral and cellular genes. [provided by RefSeq, Oct 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HIVEP1	NM_002114.4	c.95-2568G>A		intron_variant		ENST00000379388.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HIVEP1	ENST00000379388.7	c.95-2568G>A		intron_variant		1	NM_002114.4	P2

Frequencies

GnomAD3 genomes AF: 0.0769 AC: 11696 AN: 152124 Hom.: 646 Cov.: 32

Gnomad AFR AF: 0.0201

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0719

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0403

Gnomad FIN AF: 0.0649

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0937

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

GnomAD4 genome AF: 0.0768 AC: 11693 AN: 152242 Hom.: 646 Cov.: 32 AF XY: 0.0723 AC XY: 5381 AN XY: 74432

Gnomad4 AFR AF: 0.0201

Gnomad4 AMR AF: 0.0718

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0409

Gnomad4 FIN AF: 0.0649

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.0927

Alfa AF: 0.108 Hom.: 664

Bravo AF: 0.0776

Asia WGS AF: 0.0200 AC: 70 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.60

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: rs2327514; hg19: chr6-12117555;