chr10-52307770-G-A

Variant names:

• chr10-52307770-G-A
• rs1528876
• ENST00000420193.2:n.721+1630C>T

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+1630C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0466 in 152,150 control chromosomes in the GnomAD database, including 483 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 0.047 (483 hom., cov: 33)
• Consequence: PRKG1-AS1 ENST00000420193.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420193.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRKG1-AS1	NR_038277.1		n.721+1630C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRKG1-AS1	ENST00000420193.2	TSL:3	n.721+1630C>T		intron	N/A
	PRKG1-AS1	ENST00000452247.8	TSL:5	n.1097+1630C>T		intron	N/A
	PRKG1-AS1	ENST00000649494.1		n.1100+1630C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0464 AC: 7061 AN: 152032 Hom.: 476 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0186

Gnomad ASJ AF: 0.00806

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0615

Gnomad FIN AF: 0.00236

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00113

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0466 AC: 7097 AN: 152150 Hom.: 483 Cov.: 33 AF XY: 0.0467 AC XY: 3472 AN XY: 74402

African (AFR) AF: 0.150 AC: 6223 AN: 41500

American (AMR) AF: 0.0185 AC: 283 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00806 AC: 28 AN: 3472

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5168

South Asian (SAS) AF: 0.0608 AC: 293 AN: 4822

European-Finnish (FIN) AF: 0.00236 AC: 25 AN: 10582

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00113 AC: 77 AN: 67988

Other (OTH) AF: 0.0431 AC: 91 AN: 2112

Alfa AF: 0.0302 Hom.: 41

Bravo AF: 0.0518

Asia WGS AF: 0.0610 AC: 209 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.24
PhyloP100		-0.45

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1528876;

hg19: chr10-54067530;