8-78488803-A-G

Variant names:

• chr8-78488803-A-G
• rs1520333
• ENST00000522807.5:n.172-8468T>C

Variant summary

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

The ENST00000522807.5(PKIA-AS1):​n.172-8468T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,820 control chromosomes in the GnomAD database, including 14,482 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 0.39 (14482 hom., cov: 32)
• Consequence: PKIA-AS1 ENST00000522807.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.57
• Publications: 32 publications found

Genes affected

PKIA-AS1 (HGNC:51659): (PKIA antisense RNA 1)

ENSG00000286675 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522807.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKIA-AS1	ENST00000522807.5	TSL:3	n.172-8468T>C		intron	N/A
	PKIA-AS1	ENST00000653339.1		n.144+19482T>C		intron	N/A
	PKIA-AS1	ENST00000669183.1		n.201+19482T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59841 AN: 151702 Hom.: 14456 Cov.: 32

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.395 AC: 59928 AN: 151820 Hom.: 14482 Cov.: 32 AF XY: 0.398 AC XY: 29496 AN XY: 74186

African (AFR) AF: 0.681 AC: 28210 AN: 41444

American (AMR) AF: 0.286 AC: 4347 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1182 AN: 3468

East Asian (EAS) AF: 0.482 AC: 2477 AN: 5136

South Asian (SAS) AF: 0.373 AC: 1797 AN: 4814

European-Finnish (FIN) AF: 0.307 AC: 3245 AN: 10568

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17657 AN: 67876

Other (OTH) AF: 0.377 AC: 791 AN: 2100

Alfa AF: 0.325 Hom.: 16979

Bravo AF: 0.403

Asia WGS AF: 0.459 AC: 1595 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.021
DANN	Benign	0.56
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs1520333; hg19: chr8-79401038;