12-80673072-A-G

Position:

• chr12-80673072-A-G

Variant summary

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

The NM_001145026.2(PTPRQ):​c.6603-97A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 1,450,004 control chromosomes in the GnomAD database, including 92,823 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.41 (13742 hom., cov: 32)
  • Exomes 𝑓: 0.34 (79081 hom.)
• Consequence: PTPRQ NM_001145026.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.31

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]

LOC105369867 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 12-80673072-A-G is Benign according to our data. Variant chr12-80673072-A-G is described in ClinVar as [Benign]. Clinvar id is 1271771.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRQ	NM_001145026.2	c.6603-97A>G		intron_variant		ENST00000644991.3
LOC105369867	XR_007063388.1	n.130+34037T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRQ	ENST00000644991.3	c.6603-97A>G		intron_variant			NM_001145026.2	P2
PTPRQ	ENST00000616559.4	c.6702-97A>G		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61628 AN: 151866 Hom.: 13716 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.361

GnomAD4 exome AF: 0.345 AC: 447472 AN: 1298020 Hom.: 79081 AF XY: 0.342 AC XY: 216816 AN XY: 634658

Gnomad4 AFR exome AF: 0.620

Gnomad4 AMR exome AF: 0.305

Gnomad4 ASJ exome AF: 0.340

Gnomad4 EAS exome AF: 0.268

Gnomad4 SAS exome AF: 0.272

Gnomad4 FIN exome AF: 0.351

Gnomad4 NFE exome AF: 0.345

Gnomad4 OTH exome AF: 0.344

GnomAD4 genome AF: 0.406 AC: 61699 AN: 151984 Hom.: 13742 Cov.: 32 AF XY: 0.402 AC XY: 29835 AN XY: 74292

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.361

Alfa AF: 0.334 Hom.: 8341

Bravo AF: 0.413

Asia WGS AF: 0.255 AC: 886 AN: 3474

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

Jul 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs950124; hg19: chr12-81066851; COSMIC: COSV57038982;