12-80444574-T-TATATG

Position:

• chr12-80444574-T-TATATG

Variant summary

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

The NM_001145026.2(PTPRQ):​c.55-163_55-162insGATAT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,654 control chromosomes in the GnomAD database, including 3,260 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.15 (3260 hom., cov: 29)
• Consequence: PTPRQ NM_001145026.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.115

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 12-80444574-T-TATATG is Benign according to our data. Variant chr12-80444574-T-TATATG is described in ClinVar as [Benign]. Clinvar id is 1280519.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPRQ	NM_001145026.2	c.55-163_55-162insGATAT		intron_variant		ENST00000644991.3	NP_001138498.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPRQ	ENST00000644991.3	c.55-163_55-162insGATAT		intron_variant			NM_001145026.2	ENSP00000495607	P2

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23197 AN: 151536 Hom.: 3240 Cov.: 29

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0905

Gnomad ASJ AF: 0.0911

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0582

Gnomad FIN AF: 0.0309

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0728

Gnomad OTH AF: 0.131

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.153 AC: 23257 AN: 151654 Hom.: 3260 Cov.: 29 AF XY: 0.148 AC XY: 10985 AN XY: 74128

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.0904

Gnomad4 ASJ AF: 0.0911

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0584

Gnomad4 FIN AF: 0.0309

Gnomad4 NFE AF: 0.0728

Gnomad4 OTH AF: 0.129

Alfa AF: 0.117 Hom.: 234

Bravo AF: 0.169

Asia WGS AF: 0.0480 AC: 166 AN: 3472

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

Dec 17, 2018

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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: rs112125750; hg19: chr12-80838354;