12-6479279-A-G

Variant names:

• chr12-6479279-A-G
• rs2008134
• ENST00000541242.1:n.1566A>G

Variant summary

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

The ENST00000541242.1(ENSG00000256913):​n.1566A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.288 in 1,018,330 control chromosomes in the GnomAD database, including 45,174 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 0.24 (5333 hom., cov: 31)
  • Exomes 𝑓: 0.30 (39841 hom.)
• Consequence: ENSG00000256913 ENST00000541242.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.62
• Publications: 9 publications found

Genes affected

ENSG00000256913 (HGNC:):

PKP2P1 (HGNC:13413):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PKP2P1		n.6479279A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256913	ENST00000541242.1	n.1566A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36177 AN: 151948 Hom.: 5336 Cov.: 31

Gnomad AFR AF: 0.0606

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.259

GnomAD4 exome AF: 0.297 AC: 257380 AN: 866264 Hom.: 39841 Cov.: 12 AF XY: 0.300 AC XY: 136561 AN XY: 454508

African (AFR) AF: 0.0513 AC: 1150 AN: 22410

American (AMR) AF: 0.155 AC: 6738 AN: 43598

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 6540 AN: 22330

East Asian (EAS) AF: 0.345 AC: 12728 AN: 36892

South Asian (SAS) AF: 0.313 AC: 23239 AN: 74286

European-Finnish (FIN) AF: 0.300 AC: 15518 AN: 51772

Middle Eastern (MID) AF: 0.294 AC: 1320 AN: 4486

European-Non Finnish (NFE) AF: 0.313 AC: 178479 AN: 569866

Other (OTH) AF: 0.287 AC: 11668 AN: 40624

GnomAD4 genome AF: 0.238 AC: 36176 AN: 152066 Hom.: 5333 Cov.: 31 AF XY: 0.239 AC XY: 17722 AN XY: 74304

African (AFR) AF: 0.0605 AC: 2509 AN: 41502

American (AMR) AF: 0.221 AC: 3377 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1000 AN: 3468

East Asian (EAS) AF: 0.332 AC: 1713 AN: 5166

South Asian (SAS) AF: 0.320 AC: 1539 AN: 4812

European-Finnish (FIN) AF: 0.313 AC: 3302 AN: 10556

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21769 AN: 67956

Other (OTH) AF: 0.259 AC: 547 AN: 2114

Alfa AF: 0.243 Hom.: 1005

Bravo AF: 0.221

Asia WGS AF: 0.238 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	2.1
DANN	Benign	0.23
PhyloP100		3.6

Splicing

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

Other links and lift over

dbSNP: rs2008134; hg19: chr12-6588445;