12-80444133-T-TA

Position:

• chr12-80444133-T-TA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The ENST00000616559.4(PTPRQ):​c.180+221_180+222insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00218 in 278,800 control chromosomes in the GnomAD database, including 7 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0036 (5 hom., cov: 28)
  • Exomes 𝑓: 0.00068 (2 hom.)
• Consequence: PTPRQ ENST00000616559.4 intron
• Clinical Significance: Likely 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 -10 ACMG points.

• BP6: Variant 12-80444133-T-TA is Benign according to our data. Variant chr12-80444133-T-TA is described in ClinVar as [Likely_benign]. Clinvar id is 1212235.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00364 (514/141110) while in subpopulation AFR AF= 0.0126 (502/39948). AF 95% confidence interval is 0.0117. There are 5 homozygotes in gnomad4. There are 233 alleles in male gnomad4 subpopulation. Median coverage is 28. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 5 SD gene

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+221_918+222insA		intron_variant		5		ENSP00000448844
PTPRQ	ENST00000551042.5	c.660+221_660+222insA		intron_variant		5		ENSP00000447522
PTPRQ	ENST00000551573.5	c.708+221_708+222insA		intron_variant		3		ENSP00000449133
PTPRQ	ENST00000616559.4	c.180+221_180+222insA		intron_variant		5		ENSP00000483259	A2

Frequencies

GnomAD3 genomes AF: 0.00360 AC: 507 AN: 141002 Hom.: 5 Cov.: 28

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000695

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00104

GnomAD4 exome AF: 0.000683 AC: 94 AN: 137690 Hom.: 2 Cov.: 0 AF XY: 0.000565 AC XY: 42 AN XY: 74276

Gnomad4 AFR exome AF: 0.0302

Gnomad4 AMR exome AF: 0.00180

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000916

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00175

GnomAD4 genome AF: 0.00364 AC: 514 AN: 141110 Hom.: 5 Cov.: 28 AF XY: 0.00338 AC XY: 233 AN XY: 68848

Gnomad4 AFR AF: 0.0126

Gnomad4 AMR AF: 0.000694

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00103

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 13, 2020

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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: rs1565706749; hg19: chr12-80837913;