12-80444134-T-A

Position:

• chr12-80444134-T-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000616559.4(PTPRQ):​c.180+222T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0287 in 280,138 control chromosomes in the GnomAD database, including 670 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.051 (617 hom., cov: 28)
  • Exomes 𝑓: 0.0062 (53 hom.)
• Consequence: PTPRQ ENST00000616559.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.66

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 12-80444134-T-A is Benign according to our data. Variant chr12-80444134-T-A is described in ClinVar as [Benign]. Clinvar id is 1246491.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 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
PTPRQ	ENST00000547376.5	c.918+222T>A		intron_variant		5		ENSP00000448844
PTPRQ	ENST00000551042.5	c.660+222T>A		intron_variant		5		ENSP00000447522
PTPRQ	ENST00000551573.5	c.708+222T>A		intron_variant		3		ENSP00000449133
PTPRQ	ENST00000616559.4	c.180+222T>A		intron_variant		5		ENSP00000483259	A2

Frequencies

GnomAD3 genomes AF: 0.0508 AC: 7158 AN: 140920 Hom.: 613 Cov.: 28

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0223

Gnomad ASJ AF: 0.000608

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00113

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00333

Gnomad NFE AF: 0.000598

Gnomad OTH AF: 0.0312

GnomAD4 exome AF: 0.00624 AC: 868 AN: 139112 Hom.: 53 Cov.: 0 AF XY: 0.00524 AC XY: 393 AN XY: 75026

Gnomad4 AFR exome AF: 0.257

Gnomad4 AMR exome AF: 0.0180

Gnomad4 ASJ exome AF: 0.000850

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000361

Gnomad4 OTH exome AF: 0.0158

GnomAD4 genome AF: 0.0509 AC: 7174 AN: 141026 Hom.: 617 Cov.: 28 AF XY: 0.0497 AC XY: 3421 AN XY: 68816

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.0222

Gnomad4 ASJ AF: 0.000608

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00113

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000599

Gnomad4 OTH AF: 0.0308

Alfa AF: 0.00683 Hom.: 1

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 18, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.0
DANN	Benign	0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs868333045; hg19: chr12-80837914;