rs1528877

chr10-52311582-A-G

Variant summary

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

The NR_038277.1(PRKG1-AS1):n.583+1816T>C variant causes a intron, non coding transcript 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 NR_038277.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

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=-0.93).
• 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/exons	MANE	UniProt
PRKG1-AS1	NR_038277.1	n.583+1816T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRKG1-AS1	ENST00000452247.7	n.130+1816T>C		intron_variant, non_coding_transcript_variant		5
PRKG1-AS1	ENST00000420193.1	n.583+1816T>C		intron_variant, non_coding_transcript_variant		3
PRKG1-AS1	ENST00000649494.1	n.962+1816T>C		intron_variant, non_coding_transcript_variant
PRKG1-AS1	ENST00000658196.1	n.81+1816T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0946

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.380

Alfa AF: 0.438 Hom.: 13305

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1528877; hg19: chr10-54071342;