rs2156236

chr18-8022575-A-Gchr18-8022575-A-T

Variant summary

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

The NM_001105244.2(PTPRM):c.1133-47111A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 151,976 control chromosomes in the GnomAD database, including 28,610 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 0.61 (28610 hom., cov: 31)
• Consequence: PTPRM NM_001105244.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

Genes affected

PTPRM (HGNC:9675): (protein tyrosine phosphatase receptor type M) 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 has been shown to mediate cell-cell aggregation through the interaction with another molecule of this PTP on an adjacent cell. This PTP can interact with scaffolding protein RACK1/GNB2L1, which may be necessary for the downstream signaling in response to cell-cell adhesion. Alternative splicing results in multiple transcripts encoding distinct isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRM	NM_001105244.2	c.1133-47111A>G		intron_variant		ENST00000580170.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRM	ENST00000580170.6	c.1133-47111A>G		intron_variant		1	NM_001105244.2	A1

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92962 AN: 151858 Hom.: 28583 Cov.: 31

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.612 AC: 93040 AN: 151976 Hom.: 28610 Cov.: 31 AF XY: 0.609 AC XY: 45265 AN XY: 74288

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.607

Alfa AF: 0.630 Hom.: 23069

Bravo AF: 0.610

Asia WGS AF: 0.510 AC: 1775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.4
Dann	Benign	0.47

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

Publications

LitVar

Other links and lift over

dbSNP: rs2156236; hg19: chr18-8022573;