chr12-80444345-G-A

Variant names:

• chr12-80444345-G-A
• rs538419954
• NM_001145026.2:c.-1G>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001145026.2(PTPRQ):​c.-1G>A variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.000868 in 1,427,100 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.00092 (1 hom., cov: 32)
  • Exomes 𝑓: 0.00086 (1 hom.)
• Consequence: PTPRQ NM_001145026.2 5_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.93

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 Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRQ	NM_001145026.2	c.-1G>A		5_prime_UTR_variant	Exon 1 of 45	ENST00000644991.3	NP_001138498.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRQ	ENST00000644991	c.-1G>A		5_prime_UTR_variant	Exon 1 of 45		NM_001145026.2	ENSP00000495607.1

Frequencies

GnomAD3 genomes AF: 0.000924 AC: 140 AN: 151472 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.0000726

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000660

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00445

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00129

Gnomad OTH AF: 0.000481

GnomAD3 exomes AF: 0.000858 AC: 130 AN: 151566 Hom.: 0 AF XY: 0.000758 AC XY: 61 AN XY: 80442

Gnomad AFR exome AF: 0.000129

Gnomad AMR exome AF: 0.0000825

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000446

Gnomad FIN exome AF: 0.00422

Gnomad NFE exome AF: 0.00104

Gnomad OTH exome AF: 0.000234

GnomAD4 exome AF: 0.000862 AC: 1099 AN: 1275512 Hom.: 1 Cov.: 21 AF XY: 0.000890 AC XY: 565 AN XY: 635076

Gnomad4 AFR exome AF: 0.0000722

Gnomad4 AMR exome AF: 0.0000286

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000395

Gnomad4 FIN exome AF: 0.00369

Gnomad4 NFE exome AF: 0.000923

Gnomad4 OTH exome AF: 0.000280

GnomAD4 genome AF: 0.000924 AC: 140 AN: 151588 Hom.: 1 Cov.: 32 AF XY: 0.000945 AC XY: 70 AN XY: 74088

Gnomad4 AFR AF: 0.0000724

Gnomad4 AMR AF: 0.0000659

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00445

Gnomad4 NFE AF: 0.00129

Gnomad4 OTH AF: 0.000476

Alfa AF: 0.00100 Hom.: 1

Bravo AF: 0.000533

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Feb 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	20
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs538419954; hg19: chr12-80838125;