10-52309144-C-T

Variant names:

• chr10-52309144-C-T
• rs1896368
• ENST00000420193.2:n.721+256G>A

Variant summary

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

The ENST00000420193.2(PRKG1-AS1):​n.721+256G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,554 control chromosomes in the GnomAD database, including 15,417 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 0.43 (15417 hom., cov: 32)
• Consequence: PRKG1-AS1 ENST00000420193.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.676
• Publications: 18 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKG1-AS1	NR_038277.1	n.721+256G>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRKG1-AS1	ENST00000420193.2	n.721+256G>A		intron_variant	Intron 3 of 8	3
PRKG1-AS1	ENST00000452247.8	n.1097+256G>A		intron_variant	Intron 3 of 6	5
PRKG1-AS1	ENST00000649494.1	n.1100+256G>A		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65691 AN: 151440 Hom.: 15408 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.434 AC: 65721 AN: 151554 Hom.: 15417 Cov.: 32 AF XY: 0.432 AC XY: 31974 AN XY: 74090

African (AFR) AF: 0.308 AC: 12609 AN: 40998

American (AMR) AF: 0.395 AC: 6032 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1592 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2047 AN: 5170

South Asian (SAS) AF: 0.478 AC: 2306 AN: 4828

European-Finnish (FIN) AF: 0.449 AC: 4738 AN: 10562

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.511 AC: 34707 AN: 67950

Other (OTH) AF: 0.452 AC: 952 AN: 2106

Alfa AF: 0.483 Hom.: 35192

Bravo AF: 0.422

Asia WGS AF: 0.445 AC: 1549 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.37
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs1896368; hg19: chr10-54068904;