rs1528877

Variant names:

• chr10-52311582-A-G
• rs1528877
• ENST00000420193.2:n.583+1816T>C

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+1816T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,096 control chromosomes in the GnomAD database, including 11,494 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 0.35 (11494 hom., cov: 32)
• Consequence: PRKG1-AS1 ENST00000420193.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 7 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 (NFE) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKG1-AS1	NR_038277.1	n.583+1816T>C		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+1816T>C		intron_variant	Intron 2 of 8	3
PRKG1-AS1	ENST00000452247.8	n.959+1816T>C		intron_variant	Intron 2 of 6	5
PRKG1-AS1	ENST00000649494.1	n.962+1816T>C		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53180 AN: 151978 Hom.: 11495 Cov.: 32

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.350 AC: 53169 AN: 152096 Hom.: 11494 Cov.: 32 AF XY: 0.349 AC XY: 25949 AN XY: 74334

African (AFR) AF: 0.0946 AC: 3929 AN: 41538

American (AMR) AF: 0.371 AC: 5663 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1911 AN: 3468

East Asian (EAS) AF: 0.289 AC: 1495 AN: 5168

South Asian (SAS) AF: 0.313 AC: 1508 AN: 4820

European-Finnish (FIN) AF: 0.453 AC: 4784 AN: 10564

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.479 AC: 32542 AN: 67948

Other (OTH) AF: 0.380 AC: 802 AN: 2110

Alfa AF: 0.437 Hom.: 15684

Bravo AF: 0.334

Asia WGS AF: 0.245 AC: 854 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	0.28
DANN	Benign	0.61
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1528877; hg19: chr10-54071342;