rs11001553

Variant names:

• chr10-52313141-C-T
• rs11001553
• ENST00000837178.1:n.254G>A

Variant summary

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

The ENST00000837178.1(PRKG1-AS1):​n.254G>A variant causes a non coding transcript exon 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 ENST00000837178.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 8 publications found

Genes affected

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

ENSG00000308923 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PRKG1-AS1	NR_038277.1	n.583+257G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRKG1-AS1	ENST00000837178.1	n.254G>A		non_coding_transcript_exon_variant	Exon 1 of 4
PRKG1-AS1	ENST00000837186.1	n.406G>A		non_coding_transcript_exon_variant	Exon 3 of 3
PRKG1-AS1	ENST00000837187.1	n.666G>A		non_coding_transcript_exon_variant	Exon 3 of 3

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

African (AFR) AF: 0.177 AC: 7335 AN: 41480

American (AMR) AF: 0.0836 AC: 1279 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0626 AC: 217 AN: 3468

East Asian (EAS) AF: 0.104 AC: 539 AN: 5174

South Asian (SAS) AF: 0.222 AC: 1072 AN: 4818

European-Finnish (FIN) AF: 0.0502 AC: 531 AN: 10582

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6948 AN: 67990

Other (OTH) AF: 0.119 AC: 251 AN: 2114

Alfa AF: 0.107 Hom.: 1219

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11001553; hg19: chr10-54072901;