rs1941141

Variant names:

• chr18-7630984-A-G
• rs1941141
• NM_001105244.2:c.73+63093A>G

Your query was ambiguous. Multiple possible variants found:

• chr18-7630984-A-G
• chr18-7630984-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PTPRM	NM_001105244.2	c.73+63093A>G		intron_variant	Intron 1 of 32	ENST00000580170.6	NP_001098714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRM	ENST00000580170.6	c.73+63093A>G		intron_variant	Intron 1 of 32	1	NM_001105244.2	ENSP00000463325.1
PTPRM	ENST00000332175.12	c.73+63093A>G		intron_variant	Intron 1 of 30	1		ENSP00000331418.8

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

African (AFR) AF: 0.849 AC: 35194 AN: 41474

American (AMR) AF: 0.396 AC: 6056 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1076 AN: 3464

East Asian (EAS) AF: 0.714 AC: 3678 AN: 5152

South Asian (SAS) AF: 0.506 AC: 2434 AN: 4814

European-Finnish (FIN) AF: 0.117 AC: 1236 AN: 10596

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11265 AN: 67978

Other (OTH) AF: 0.373 AC: 787 AN: 2112

Alfa AF: 0.250 Hom.: 14013

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
PhyloP100		-1.8
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: rs1941141; hg19: chr18-7630982;