rs12211360

chr6-142798695-A-G

Variant summary

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

The NM_006734.4(HIVEP2):c.-527-15080T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,186 control chromosomes in the GnomAD database, including 1,376 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 0.12 (1376 hom., cov: 32)
• Consequence: HIVEP2 NM_006734.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67

Genes affected

HIVEP2 (HGNC:4921): (HIVEP zinc finger 2) This gene encodes a member of a family of closely related, large, zinc finger-containing transcription factors. The encoded protein regulates transcription by binding to regulatory regions of various cellular and viral genes that maybe involved in growth, development and metastasis. The protein contains the ZAS domain comprised of two widely separated regions of zinc finger motifs, a stretch of highly acidic amino acids and a serine/threonine-rich sequence. [provided by RefSeq, Nov 2012]

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 (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HIVEP2	NM_006734.4	c.-527-15080T>C		intron_variant		ENST00000367603.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HIVEP2	ENST00000367603.8	c.-527-15080T>C		intron_variant		1	NM_006734.4	P1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18120 AN: 152066 Hom.: 1378 Cov.: 32

Gnomad AFR AF: 0.0313

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0305

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.119 AC: 18101 AN: 152186 Hom.: 1376 Cov.: 32 AF XY: 0.118 AC XY: 8759 AN XY: 74394

Gnomad4 AFR AF: 0.0311

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0306

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.137

Alfa AF: 0.145 Hom.: 403

Bravo AF: 0.112

Asia WGS AF: 0.0970 AC: 337 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	6.1
Dann	Benign	0.42

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: rs12211360; hg19: chr6-143119832;