rs9380062

Variant names:

• chr6-28169791-G-A
• rs9380062
• ENST00000562227.2:c.*576G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-28169791-G-A
• chr6-28169791-G-T

Variant summary

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

The ENST00000562227.2(ZKSCAN8P1):​c.*576G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 151,972 control chromosomes in the GnomAD database, including 4,142 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 0.23 (4142 hom., cov: 32)
• Consequence: ZKSCAN8P1 ENST00000562227.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552

Genes affected

ZKSCAN8P1 (HGNC:18777): (ZKSCAN8 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZKSCAN8P1	NR_103448.1	n.*196G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZKSCAN8P1	ENST00000562227.2	c.*576G>A		downstream_gene_variant		3		ENSP00000510811.1
ZKSCAN8P1	ENST00000440790.6	c.*576G>A		downstream_gene_variant		5		ENSP00000509393.1

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34820 AN: 151854 Hom.: 4135 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.229 AC: 34856 AN: 151972 Hom.: 4142 Cov.: 32 AF XY: 0.224 AC XY: 16622 AN XY: 74288

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.220

Alfa AF: 0.222 Hom.: 1384

Bravo AF: 0.240

Asia WGS AF: 0.154 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.58
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9380062; hg19: chr6-28137569;