rs10484256

Variant names:

• chr6-12194917-A-G
• rs10484256
• ENST00000789282.1:n.116-10607T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000789282.1(ENSG00000302734):​n.116-10607T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,276 control chromosomes in the GnomAD database, including 2,058 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 (2058 hom., cov: 32)
• Consequence: ENSG00000302734 ENST00000789282.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570
• Publications: 3 publications found

Genes affected

ENSG00000302734 (HGNC:):

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

Our verdict: Benign. The variant received -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 = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HIVEP1	XR_007059258.1	n.7531-4304A>G		intron_variant	Intron 10 of 11
HIVEP1	XR_007059259.1	n.6799-4304A>G		intron_variant	Intron 8 of 9
HIVEP1	XR_007059260.1	n.6741-4304A>G		intron_variant	Intron 8 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302734	ENST00000789282.1	n.116-10607T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22912 AN: 152158 Hom.: 2060 Cov.: 32

Gnomad AFR AF: 0.0718

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0329

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.150 AC: 22917 AN: 152276 Hom.: 2058 Cov.: 32 AF XY: 0.148 AC XY: 11052 AN XY: 74458

African (AFR) AF: 0.0720 AC: 2992 AN: 41572

American (AMR) AF: 0.138 AC: 2109 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 646 AN: 3472

East Asian (EAS) AF: 0.0331 AC: 172 AN: 5190

South Asian (SAS) AF: 0.181 AC: 875 AN: 4824

European-Finnish (FIN) AF: 0.128 AC: 1360 AN: 10602

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.209 AC: 14223 AN: 68010

Other (OTH) AF: 0.175 AC: 369 AN: 2112

Alfa AF: 0.169 Hom.: 390

Bravo AF: 0.146

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.59
DANN	Benign	0.53
PhyloP100		-0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10484256; hg19: chr6-12195150;