rs1446083

chr18-7770952-A-G

Variant summary

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

The NM_001105244.2(PTPRM):c.74-3197A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0977 in 152,238 control chromosomes in the GnomAD database, including 2,189 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 0.098 (2189 hom., cov: 32)
• Consequence: PTPRM NM_001105244.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.891

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=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRM	NM_001105244.2	c.74-3197A>G		intron_variant		ENST00000580170.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRM	ENST00000580170.6	c.74-3197A>G		intron_variant		1	NM_001105244.2	A1
PTPRM	ENST00000332175.12	c.74-3197A>G		intron_variant		1		P4
PTPRM	ENST00000400053.8	c.-113-3197A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0975 AC: 14825 AN: 152120 Hom.: 2180 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0423

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.0957

Gnomad SAS AF: 0.00868

Gnomad FIN AF: 0.00716

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00332

Gnomad OTH AF: 0.0765

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

GnomAD4 genome AF: 0.0977 AC: 14868 AN: 152238 Hom.: 2189 Cov.: 32 AF XY: 0.0957 AC XY: 7128 AN XY: 74454

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.0422

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.0959

Gnomad4 SAS AF: 0.00828

Gnomad4 FIN AF: 0.00716

Gnomad4 NFE AF: 0.00332

Gnomad4 OTH AF: 0.0762

Alfa AF: 0.0612 Hom.: 285

Bravo AF: 0.111

Asia WGS AF: 0.0650 AC: 225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	13
Dann	Benign	0.86

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: rs1446083; hg19: chr18-7770950;