10-52309426-C-T

Position:

• chr10-52309426-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.695G>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 0.29 in 151,882 control chromosomes in the GnomAD database, including 8,076 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 0.29 (8075 hom., cov: 32)
  • Exomes 𝑓: 0.38 (1 hom.)
• Consequence: PRKG1-AS1 NR_038277.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRKG1-AS1	NR_038277.1	n.695G>A		non_coding_transcript_exon_variant	3/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRKG1-AS1	ENST00000452247.7	n.242G>A		non_coding_transcript_exon_variant	3/7	5
PRKG1-AS1	ENST00000420193.1	n.695G>A		non_coding_transcript_exon_variant	3/6	3
PRKG1-AS1	ENST00000649494.1	n.1074G>A		non_coding_transcript_exon_variant	3/8
PRKG1-AS1	ENST00000658196.1	n.193G>A		non_coding_transcript_exon_variant	2/5

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44021 AN: 151754 Hom.: 8079 Cov.: 32

Gnomad AFR AF: 0.0768

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.317

GnomAD4 exome AF: 0.375 AC: 3 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 3 AN XY: 6

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.750

GnomAD4 genome AF: 0.290 AC: 44005 AN: 151874 Hom.: 8075 Cov.: 32 AF XY: 0.289 AC XY: 21455 AN XY: 74206

Gnomad4 AFR AF: 0.0765

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.314

Alfa AF: 0.384 Hom.: 7245

Bravo AF: 0.275

Asia WGS AF: 0.208 AC: 723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1896367; hg19: chr10-54069186;