rs13218440

Positions:

• chr6-12059721-G-A
• chr6-12059721-G-C
• chr6-12059721-G-T

Variant summary

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

The NM_002114.4(HIVEP1):​c.41-29463G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,746 control chromosomes in the GnomAD database, including 12,257 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 0.40 (12257 hom., cov: 31)
• Consequence: HIVEP1 NM_002114.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238

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]

HIVEP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HIVEP1	NM_002114.4	c.41-29463G>A		intron_variant		ENST00000379388.7	NP_002105.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HIVEP1	ENST00000379388.7	c.41-29463G>A		intron_variant		1	NM_002114.4	ENSP00000368698.2

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61184 AN: 151628 Hom.: 12247 Cov.: 31

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.404 AC: 61233 AN: 151746 Hom.: 12257 Cov.: 31 AF XY: 0.404 AC XY: 29941 AN XY: 74100

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.423

Alfa AF: 0.399 Hom.: 20495

Bravo AF: 0.407

Asia WGS AF: 0.385 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.6
DANN	Benign	0.47

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: rs13218440; hg19: chr6-12059954;