rs11001553

Positions:

• chr10-52313141-C-T

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+257G>A 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 0.121 in 152,120 control chromosomes in the GnomAD database, including 1,303 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 0.12 (1303 hom., cov: 32)
• Consequence: PRKG1-AS1 NR_038277.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRKG1-AS1	NR_038277.1	n.583+257G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRKG1-AS1	ENST00000452247.7	n.130+257G>A		intron_variant, non_coding_transcript_variant		5
PRKG1-AS1	ENST00000420193.1	n.583+257G>A		intron_variant, non_coding_transcript_variant		3
PRKG1-AS1	ENST00000649494.1	n.962+257G>A		intron_variant, non_coding_transcript_variant
PRKG1-AS1	ENST00000658196.1	n.81+257G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18401 AN: 152002 Hom.: 1298 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.0626

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0502

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.121 AC: 18433 AN: 152120 Hom.: 1303 Cov.: 32 AF XY: 0.120 AC XY: 8920 AN XY: 74360

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0836

Gnomad4 ASJ AF: 0.0626

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.0502

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.119

Alfa AF: 0.104 Hom.: 866

Bravo AF: 0.123

Asia WGS AF: 0.212 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.32
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11001553; hg19: chr10-54072901;