chr10-6583416-T-C

Variant names:

• chr10-6583416-T-C
• rs2255088
• ENST00000445427.2:n.510-260T>C

Variant summary

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

The ENST00000445427.2(PRKCQ-AS1):​n.510-260T>C variant causes a intron 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 ENST00000445427.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PRKCQ-AS1	NR_036502.1	n.568-260T>C		intron_variant	Intron 2 of 2
PRKCQ-AS1	NR_036503.1	n.504-260T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRKCQ-AS1	ENST00000445427.2	n.510-260T>C		intron_variant	Intron 1 of 1	1
PRKCQ-AS1	ENST00000455810.5	n.568-260T>C		intron_variant	Intron 2 of 2	2
PRKCQ-AS1	ENST00000613651.3	n.488-260T>C		intron_variant	Intron 2 of 2	2

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

African (AFR) AF: 0.514 AC: 21334 AN: 41472

American (AMR) AF: 0.410 AC: 6259 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 889 AN: 3468

East Asian (EAS) AF: 0.411 AC: 2124 AN: 5166

South Asian (SAS) AF: 0.270 AC: 1301 AN: 4822

European-Finnish (FIN) AF: 0.343 AC: 3626 AN: 10578

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22426 AN: 67972

Other (OTH) AF: 0.399 AC: 842 AN: 2110

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2255088; hg19: chr10-6625378;