6-142778142-G-C

Position:

• chr6-142778142-G-C

Variant summary

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

The NM_006734.4(HIVEP2):​c.-432-1951C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,210 control chromosomes in the GnomAD database, including 1,993 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 0.15 (1993 hom., cov: 32)
• Consequence: HIVEP2 NM_006734.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HIVEP2	NM_006734.4	c.-432-1951C>G		intron_variant		ENST00000367603.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HIVEP2	ENST00000367603.8	c.-432-1951C>G		intron_variant		1	NM_006734.4	P1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23389 AN: 152092 Hom.: 1996 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0743

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.154 AC: 23374 AN: 152210 Hom.: 1993 Cov.: 32 AF XY: 0.151 AC XY: 11247 AN XY: 74422

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.0748

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.170

Alfa AF: 0.169 Hom.: 279

Bravo AF: 0.150

Asia WGS AF: 0.149 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.30
DANN	Benign	0.61

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: rs12205474; hg19: chr6-143099279;