rs1941141

chr18-7630984-A-Gchr18-7630984-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.73+63093A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 152,076 control chromosomes in the GnomAD database, including 19,645 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 0.41 (19645 hom., cov: 32)
• Consequence: PTPRM NM_001105244.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRM	NM_001105244.2	c.73+63093A>G		intron_variant		ENST00000580170.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRM	ENST00000580170.6	c.73+63093A>G		intron_variant		1	NM_001105244.2	A1
PTPRM	ENST00000332175.12	c.73+63093A>G		intron_variant		1		P4

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61988 AN: 151958 Hom.: 19566 Cov.: 32

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.409 AC: 62135 AN: 152076 Hom.: 19645 Cov.: 32 AF XY: 0.412 AC XY: 30599 AN XY: 74348

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.373

Alfa AF: 0.222 Hom.: 7614

Bravo AF: 0.446

Asia WGS AF: 0.616 AC: 2139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.090
Dann	Benign	0.55

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: rs1941141; hg19: chr18-7630982;