rs7069912

Variant names:

• chr10-52311959-G-A
• rs7069912
• ENST00000420193.2:n.583+1439C>T

Variant summary

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

The ENST00000420193.2(PRKG1-AS1):​n.583+1439C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.097 in 152,190 control chromosomes in the GnomAD database, including 1,928 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 0.097 (1928 hom., cov: 32)
• Consequence: PRKG1-AS1 ENST00000420193.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 2 publications found

Genes affected

PRKG1-AS1 (HGNC:45029): (PRKG1 antisense RNA 1)

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 = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKG1-AS1	NR_038277.1	n.583+1439C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRKG1-AS1	ENST00000420193.2	n.583+1439C>T		intron_variant	Intron 2 of 8	3
PRKG1-AS1	ENST00000452247.8	n.959+1439C>T		intron_variant	Intron 2 of 6	5
PRKG1-AS1	ENST00000649494.1	n.962+1439C>T		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.0968 AC: 14723 AN: 152072 Hom.: 1920 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0574

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.0544

Gnomad FIN AF: 0.00302

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0105

Gnomad OTH AF: 0.0931

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

GnomAD4 genome AF: 0.0970 AC: 14766 AN: 152190 Hom.: 1928 Cov.: 32 AF XY: 0.0948 AC XY: 7056 AN XY: 74410

African (AFR) AF: 0.297 AC: 12333 AN: 41492

American (AMR) AF: 0.0574 AC: 877 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3470

East Asian (EAS) AF: 0.0139 AC: 72 AN: 5182

South Asian (SAS) AF: 0.0536 AC: 258 AN: 4814

European-Finnish (FIN) AF: 0.00302 AC: 32 AN: 10604

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0105 AC: 715 AN: 68016

Other (OTH) AF: 0.0945 AC: 200 AN: 2116

Alfa AF: 0.0881 Hom.: 278

Bravo AF: 0.110

Asia WGS AF: 0.0690 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.16
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7069912; hg19: chr10-54071719;