chr12-80444138-T-A

Position:

• chr12-80444138-T-A

Variant summary

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

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.964

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=-0.75).
• 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
PTPRQ	ENST00000616559.4	c.180+226T>A		intron_variant		5		ENSP00000483259.1
PTPRQ	ENST00000547376.5	c.918+226T>A		intron_variant		5		ENSP00000448844.1
PTPRQ	ENST00000551042.5	c.660+226T>A		intron_variant		5		ENSP00000447522.1
PTPRQ	ENST00000551573.5	c.708+226T>A		intron_variant		3		ENSP00000449133.1

Frequencies

GnomAD3 genomes AF: 0.0504 AC: 7127 AN: 141400 Hom.: 614 Cov.: 28

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

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

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

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	-0.75
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

Other links and lift over

dbSNP: rs548980338; hg19: chr12-80837918;