rs10150311

Variant summary

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

The NM_007039.4(PTPN21):​c.351-2108A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,082 control chromosomes in the GnomAD database, including 9,729 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 0.35 ( 9729 hom., cov: 32)

Consequence

PTPN21
NM_007039.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10
Variant links:
Genes affected
PTPN21 (HGNC:9651): (protein tyrosine phosphatase non-receptor type 21) 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 contains an N-terminal domain, similar to cytoskeletal- associated proteins including band 4.1, ezrin, merlin, and radixin. This PTP was shown to specially interact with BMX/ETK, a member of Tec tyrosine kinase family characterized by a multimodular structures including PH, SH3, and SH2 domains. The interaction of this PTP with BMX kinase was found to increase the activation of STAT3, but not STAT2 kinase. Studies of the similar gene in mice suggested the possible roles of this PTP in liver regeneration and spermatogenesis. [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=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PTPN21NM_007039.4 linkuse as main transcriptc.351-2108A>G intron_variant ENST00000556564.6
LOC105370614XR_007064296.1 linkuse as main transcriptn.166-3782T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PTPN21ENST00000556564.6 linkuse as main transcriptc.351-2108A>G intron_variant 1 NM_007039.4 P1
ENST00000555444.2 linkuse as main transcriptn.316-3782T>C intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.347
AC:
52666
AN:
151964
Hom.:
9698
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.479
Gnomad AMI
AF:
0.352
Gnomad AMR
AF:
0.246
Gnomad ASJ
AF:
0.305
Gnomad EAS
AF:
0.351
Gnomad SAS
AF:
0.343
Gnomad FIN
AF:
0.280
Gnomad MID
AF:
0.204
Gnomad NFE
AF:
0.303
Gnomad OTH
AF:
0.311
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.347
AC:
52763
AN:
152082
Hom.:
9729
Cov.:
32
AF XY:
0.342
AC XY:
25443
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.479
Gnomad4 AMR
AF:
0.247
Gnomad4 ASJ
AF:
0.305
Gnomad4 EAS
AF:
0.352
Gnomad4 SAS
AF:
0.345
Gnomad4 FIN
AF:
0.280
Gnomad4 NFE
AF:
0.303
Gnomad4 OTH
AF:
0.315
Alfa
AF:
0.331
Hom.:
2322
Bravo
AF:
0.349
Asia WGS
AF:
0.347
AC:
1209
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
8.5
DANN
Benign
0.87

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: rs10150311; hg19: chr14-88976472; API