rs2290819

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001105244.2(PTPRM):​c.3055-5926G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,982 control chromosomes in the GnomAD database, including 14,979 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 0.44 ( 14964 hom., cov: 32)
Exomes 𝑓: 0.62 ( 15 hom. )

Consequence

PTPRM
NM_001105244.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.109
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PTPRMNM_001105244.2 linkuse as main transcriptc.3055-5926G>T intron_variant ENST00000580170.6
LOC100192426NR_024419.1 linkuse as main transcriptn.289C>A non_coding_transcript_exon_variant 3/4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PTPRMENST00000580170.6 linkuse as main transcriptc.3055-5926G>T intron_variant 1 NM_001105244.2 A1P28827-2
ENST00000580491.1 linkuse as main transcriptn.289C>A non_coding_transcript_exon_variant 3/42

Frequencies

GnomAD3 genomes
AF:
0.435
AC:
66062
AN:
151796
Hom.:
14944
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.562
Gnomad AMI
AF:
0.360
Gnomad AMR
AF:
0.343
Gnomad ASJ
AF:
0.326
Gnomad EAS
AF:
0.308
Gnomad SAS
AF:
0.462
Gnomad FIN
AF:
0.425
Gnomad MID
AF:
0.370
Gnomad NFE
AF:
0.395
Gnomad OTH
AF:
0.438
GnomAD4 exome
AF:
0.618
AC:
42
AN:
68
Hom.:
15
Cov.:
0
AF XY:
0.500
AC XY:
17
AN XY:
34
show subpopulations
Gnomad4 AFR exome
AF:
0.500
Gnomad4 EAS exome
AF:
0.500
Gnomad4 FIN exome
AF:
0.795
Gnomad4 NFE exome
AF:
0.250
GnomAD4 genome
AF:
0.435
AC:
66132
AN:
151914
Hom.:
14964
Cov.:
32
AF XY:
0.432
AC XY:
32110
AN XY:
74260
show subpopulations
Gnomad4 AFR
AF:
0.562
Gnomad4 AMR
AF:
0.342
Gnomad4 ASJ
AF:
0.326
Gnomad4 EAS
AF:
0.308
Gnomad4 SAS
AF:
0.462
Gnomad4 FIN
AF:
0.425
Gnomad4 NFE
AF:
0.395
Gnomad4 OTH
AF:
0.438
Alfa
AF:
0.410
Hom.:
2623
Bravo
AF:
0.430
Asia WGS
AF:
0.410
AC:
1427
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.2
DANN
Benign
0.52

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2290819; hg19: chr18-8364962; API