rs1528288

Positions:

• chr12-80547286-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145026.2(PTPRQ):​c.4015+589G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 152,214 control chromosomes in the GnomAD database, including 69,277 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.95 (69277 hom., cov: 31)
• Consequence: PTPRQ NM_001145026.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRQ	NM_001145026.2	c.4015+589G>A		intron_variant		ENST00000644991.3
LOC105369867	XR_007063388.1	n.415+3342C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRQ	ENST00000644991.3	c.4015+589G>A		intron_variant			NM_001145026.2	P2
PTPRQ	ENST00000616559.4	c.4141+589G>A		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.952 AC: 144862 AN: 152096 Hom.: 69221 Cov.: 31

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.977

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.960

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

GnomAD4 genome AF: 0.952 AC: 144978 AN: 152214 Hom.: 69277 Cov.: 31 AF XY: 0.951 AC XY: 70739 AN XY: 74404

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.922

Gnomad4 ASJ AF: 0.993

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.931

Gnomad4 FIN AF: 0.977

Gnomad4 NFE AF: 0.987

Gnomad4 OTH AF: 0.960

Alfa AF: 0.966 Hom.: 8835

Bravo AF: 0.945

Asia WGS AF: 0.843 AC: 2934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.45
DANN	Benign	0.21

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: rs1528288; hg19: chr12-80941065;