10-6583416-T-C

Position:

• chr10-6583416-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_036502.1(PRKCQ-AS1):​n.568-260T>C 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 0.389 in 152,064 control chromosomes in the GnomAD database, including 12,053 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 0.39 (12053 hom., cov: 31)
• Consequence: PRKCQ-AS1 NR_036502.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999

Genes affected

PRKCQ-AS1 (HGNC:44689): (PRKCQ antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRKCQ-AS1	NR_036502.1	n.568-260T>C		intron_variant, non_coding_transcript_variant
PRKCQ-AS1	NR_036503.1	n.504-260T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRKCQ-AS1	ENST00000687343.1	n.423-260T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59085 AN: 151946 Hom.: 12052 Cov.: 31

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.389 AC: 59117 AN: 152064 Hom.: 12053 Cov.: 31 AF XY: 0.386 AC XY: 28696 AN XY: 74324

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.399

Alfa AF: 0.377 Hom.: 1616

Bravo AF: 0.403

Asia WGS AF: 0.369 AC: 1285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2255088; hg19: chr10-6625378;