12-80444138-T-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000551573.5(PTPRQ):​c.708+226T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0284 in 282,240 control chromosomes in the GnomAD database, including 676 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.050 ( 618 hom., cov: 28)
Exomes 𝑓: 0.0063 ( 58 hom. )

Consequence

PTPRQ
ENST00000551573.5 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.964
Variant links:
Genes affected
PTPRQ (HGNC:9679): (protein tyrosine phosphatase receptor type Q) This locus encodes a member of the type III receptor-like protein-tyrosine phosphatase family. The encoded protein catalyzes the dephosphorylation of phosphotyrosine and phosphatidylinositol and plays roles in cellular proliferation and differentiation. Mutations at this locus have been linked to autosomal recessive deafness. [provided by RefSeq, Mar 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 12-80444138-T-A is Benign according to our data. Variant chr12-80444138-T-A is described in ClinVar as [Benign]. Clinvar id is 1276682.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PTPRQENST00000616559.4 linkc.180+226T>A intron_variant 5 ENSP00000483259.1 A0A087X0B9
PTPRQENST00000547376.5 linkc.918+226T>A intron_variant 5 ENSP00000448844.1 F8VXI2
PTPRQENST00000551042.5 linkc.660+226T>A intron_variant 5 ENSP00000447522.1 F8W122
PTPRQENST00000551573.5 linkc.708+226T>A intron_variant 3 ENSP00000449133.1 F8VW52

Frequencies

GnomAD3 genomes
AF:
0.0504
AC:
7127
AN:
141400
Hom.:
614
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.169
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0221
Gnomad ASJ
AF:
0.000608
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00112
Gnomad FIN
AF:
0.000109
Gnomad MID
AF:
0.00333
Gnomad NFE
AF:
0.000597
Gnomad OTH
AF:
0.0319
GnomAD4 exome
AF:
0.00629
AC:
885
AN:
140732
Hom.:
58
Cov.:
0
AF XY:
0.00532
AC XY:
404
AN XY:
75982
show subpopulations
Gnomad4 AFR exome
AF:
0.259
Gnomad4 AMR exome
AF:
0.0175
Gnomad4 ASJ exome
AF:
0.000840
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000494
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000404
Gnomad4 OTH exome
AF:
0.0164
GnomAD4 genome
AF:
0.0505
AC:
7142
AN:
141508
Hom.:
618
Cov.:
28
AF XY:
0.0494
AC XY:
3414
AN XY:
69130
show subpopulations
Gnomad4 AFR
AF:
0.168
Gnomad4 AMR
AF:
0.0221
Gnomad4 ASJ
AF:
0.000608
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00112
Gnomad4 FIN
AF:
0.000109
Gnomad4 NFE
AF:
0.000597
Gnomad4 OTH
AF:
0.0315
Alfa
AF:
0.00683
Hom.:
1

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxAug 18, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
6.2
DANN
Benign
0.76

Splicing

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: rs548980338; hg19: chr12-80837918; API