chr12-80658574-T-C

Variant names:

• chr12-80658574-T-C
• rs1163016
• NM_001145026.2:c.6192+513T>C

Variant summary

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

The NM_001145026.2(PTPRQ):​c.6192+513T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,836 control chromosomes in the GnomAD database, including 22,128 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 0.50 (22128 hom., cov: 31)
• Consequence: PTPRQ NM_001145026.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRQ	NM_001145026.2	c.6192+513T>C		intron_variant	Intron 39 of 44	ENST00000644991.3	NP_001138498.1
LOC105369867	XR_007063388.1	n.130+48535A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRQ	ENST00000644991.3	c.6192+513T>C		intron_variant	Intron 39 of 44		NM_001145026.2	ENSP00000495607.1
PTPRQ	ENST00000616559.4	c.6291+513T>C		intron_variant	Intron 39 of 44	5		ENSP00000483259.1

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76072 AN: 151718 Hom.: 22083 Cov.: 31

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.502 AC: 76173 AN: 151836 Hom.: 22128 Cov.: 31 AF XY: 0.497 AC XY: 36869 AN XY: 74212

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.450

Alfa AF: 0.390 Hom.: 16438

Bravo AF: 0.516

Asia WGS AF: 0.502 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.74

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: rs1163016; hg19: chr12-81052353; COSMIC: COSV57038500; COSMIC: COSV57038500;