rs1528876

Variant names:

• chr10-52307770-G-A
• rs1528876
• ENST00000420193.1:n.721+1630C>T

Variant summary

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

The ENST00000420193.1(PRKG1-AS1):​n.721+1630C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0466 in 152,150 control chromosomes in the GnomAD database, including 483 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 0.047 (483 hom., cov: 33)
• Consequence: PRKG1-AS1 ENST00000420193.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKG1-AS1	NR_038277.1	n.721+1630C>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRKG1-AS1	ENST00000420193.1	n.721+1630C>T		intron_variant	Intron 3 of 5	3
PRKG1-AS1	ENST00000452247.7	n.268+1630C>T		intron_variant	Intron 3 of 6	5
PRKG1-AS1	ENST00000649494.1	n.1100+1630C>T		intron_variant	Intron 3 of 7
PRKG1-AS1	ENST00000658196.1	n.219+1630C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0464 AC: 7061 AN: 152032 Hom.: 476 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0186

Gnomad ASJ AF: 0.00806

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0615

Gnomad FIN AF: 0.00236

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00113

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0466 AC: 7097 AN: 152150 Hom.: 483 Cov.: 33 AF XY: 0.0467 AC XY: 3472 AN XY: 74402

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.0185

Gnomad4 ASJ AF: 0.00806

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.0608

Gnomad4 FIN AF: 0.00236

Gnomad4 NFE AF: 0.00113

Gnomad4 OTH AF: 0.0431

Alfa AF: 0.0271 Hom.: 35

Bravo AF: 0.0518

Asia WGS AF: 0.0610 AC: 209 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1528876; hg19: chr10-54067530;