12-80444130-T-TA

Position:

• chr12-80444130-T-TA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000551573.5(PTPRQ):​c.708+218_708+219insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0378 in 228,382 control chromosomes in the GnomAD database, including 798 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.055 (698 hom., cov: 27)
  • Exomes 𝑓: 0.011 (100 hom.)
• Consequence: PTPRQ ENST00000551573.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.854

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 -10 ACMG points.

• BP6: Variant 12-80444130-T-TA is Benign according to our data. Variant chr12-80444130-T-TA is described in ClinVar as [Benign]. Clinvar id is 1278282.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 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	ENST00000616559.4	c.180+218_180+219insA		intron_variant		5		ENSP00000483259.1
PTPRQ	ENST00000547376.5	c.918+218_918+219insA		intron_variant		5		ENSP00000448844.1
PTPRQ	ENST00000551042.5	c.660+218_660+219insA		intron_variant		5		ENSP00000447522.1
PTPRQ	ENST00000551573.5	c.708+218_708+219insA		intron_variant		3		ENSP00000449133.1

Frequencies

GnomAD3 genomes AF: 0.0549 AC: 7673 AN: 139850 Hom.: 693 Cov.: 27

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0231

Gnomad ASJ AF: 0.000612

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00115

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00336

Gnomad NFE AF: 0.000603

Gnomad OTH AF: 0.0333

GnomAD4 exome AF: 0.0106 AC: 936 AN: 88428 Hom.: 100 Cov.: 0 AF XY: 0.00896 AC XY: 430 AN XY: 47980

Gnomad4 AFR exome AF: 0.338

Gnomad4 AMR exome AF: 0.0307

Gnomad4 ASJ exome AF: 0.00127

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000900

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000604

Gnomad4 OTH exome AF: 0.0268

GnomAD4 genome AF: 0.0550 AC: 7696 AN: 139954 Hom.: 698 Cov.: 27 AF XY: 0.0536 AC XY: 3661 AN XY: 68256

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.0231

Gnomad4 ASJ AF: 0.000612

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00115

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000603

Gnomad4 OTH AF: 0.0330

Alfa AF: 0.0378 Hom.: 5

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs200982733; hg19: chr12-80837910;