rs2008134

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr12-6479279-A-G
• chr12-6479279-A-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000541242.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000256913	ENST00000541242.1	TSL:6	n.1566A>G		non_coding_transcript_exon	Exon 1 of 1

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 v4.9

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;