rs7069912

Positions:

• chr10-52311959-G-A

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+1439C>T 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 0.097 in 152,190 control chromosomes in the GnomAD database, including 1,928 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 0.097 (1928 hom., cov: 32)
• Consequence: PRKG1-AS1 NR_038277.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRKG1-AS1	NR_038277.1	n.583+1439C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRKG1-AS1	ENST00000452247.7	n.130+1439C>T		intron_variant, non_coding_transcript_variant		5
PRKG1-AS1	ENST00000420193.1	n.583+1439C>T		intron_variant, non_coding_transcript_variant		3
PRKG1-AS1	ENST00000649494.1	n.962+1439C>T		intron_variant, non_coding_transcript_variant
PRKG1-AS1	ENST00000658196.1	n.81+1439C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0968 AC: 14723 AN: 152072 Hom.: 1920 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0574

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.0544

Gnomad FIN AF: 0.00302

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0105

Gnomad OTH AF: 0.0931

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

GnomAD4 genome AF: 0.0970 AC: 14766 AN: 152190 Hom.: 1928 Cov.: 32 AF XY: 0.0948 AC XY: 7056 AN XY: 74410

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.0574

Gnomad4 ASJ AF: 0.0732

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.0536

Gnomad4 FIN AF: 0.00302

Gnomad4 NFE AF: 0.0105

Gnomad4 OTH AF: 0.0945

Alfa AF: 0.0881 Hom.: 278

Bravo AF: 0.110

Asia WGS AF: 0.0690 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7069912; hg19: chr10-54071719;