12-80646484-AG-AGG

Position:

• chr12-80646484-AG-AGG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001145026.2(PTPRQ):​c.5916-2409dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,086 control chromosomes in the GnomAD database, including 3,209 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.17 (3209 hom., cov: 29)
• Consequence: PTPRQ NM_001145026.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.546

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRQ	NM_001145026.2	c.5916-2409dup		intron_variant		ENST00000644991.3
LOC105369867	XR_007063388.1	n.130+60624_130+60625insC		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRQ	ENST00000644991.3	c.5916-2409dup		intron_variant			NM_001145026.2	P2
PTPRQ	ENST00000547881.1	c.200-3100dup		intron_variant		5
PTPRQ	ENST00000616559.4	c.6042-3100dup		intron_variant		5		A2
PTPRQ	ENST00000549355.1	n.405-3100dup		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26539 AN: 151968 Hom.: 3205 Cov.: 29

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.175 AC: 26574 AN: 152086 Hom.: 3209 Cov.: 29 AF XY: 0.173 AC XY: 12898 AN XY: 74374

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0521

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.157

Alfa AF: 0.142 Hom.: 272

Bravo AF: 0.190

Asia WGS AF: 0.165 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs11465200; hg19: chr12-81040263;