NM_002844.4:c.3251+978A>G

Variant names:

• chr6-127984743-T-C
• rs9402011
• NM_002844.4:c.3251+978A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_002844.4(PTPRK):​c.3251+978A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,054 control chromosomes in the GnomAD database, including 6,687 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 0.29 (6687 hom., cov: 32)
• Consequence: PTPRK NM_002844.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.902
• Publications: 5 publications found

Genes affected

PTPRK (HGNC:9674): (protein tyrosine phosphatase receptor type K) The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP possesses an extracellular region, a single transmembrane region, and two tandem catalytic domains, and thus represents a receptor-type PTP. The extracellular region contains a meprin-A5 antigen-PTP mu (MAM) domain, an Ig-like domain and four fibronectin type III-like repeats. This PTP was shown to mediate homophilic intercellular interaction, possibly through the interaction with beta- and gamma-catenin at adherens junctions. Expression of this gene was found to be stimulated by TGF-beta 1, which may be important for the inhibition of keratinocyte proliferation. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002844.4. 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
	PTPRK	NM_002844.4	MANE Select	c.3251+978A>G		intron	N/A	NP_002835.2
	PTPRK	NM_001291981.2		c.3317+978A>G		intron	N/A	NP_001278910.1
	PTPRK	NM_001135648.3		c.3269+978A>G		intron	N/A	NP_001129120.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRK	ENST00000368226.9	TSL:1 MANE Select	c.3251+978A>G		intron	N/A	ENSP00000357209.4
	PTPRK	ENST00000532331.5	TSL:1	c.3317+978A>G		intron	N/A	ENSP00000432973.1
	PTPRK	ENST00000368213.9	TSL:1	c.3269+978A>G		intron	N/A	ENSP00000357196.5

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44555 AN: 151936 Hom.: 6676 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.293 AC: 44609 AN: 152054 Hom.: 6687 Cov.: 32 AF XY: 0.296 AC XY: 22010 AN XY: 74312

African (AFR) AF: 0.267 AC: 11086 AN: 41486

American (AMR) AF: 0.320 AC: 4884 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1073 AN: 3470

East Asian (EAS) AF: 0.435 AC: 2248 AN: 5168

South Asian (SAS) AF: 0.284 AC: 1371 AN: 4822

European-Finnish (FIN) AF: 0.363 AC: 3831 AN: 10556

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19208 AN: 67966

Other (OTH) AF: 0.274 AC: 580 AN: 2114

Alfa AF: 0.287 Hom.: 26870

Bravo AF: 0.293

Asia WGS AF: 0.329 AC: 1142 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	10
DANN	Benign	0.84
PhyloP100		0.90
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9402011; hg19: chr6-128305888;