7-121888781-T-C

Position:

• chr7-121888781-T-C

Variant summary

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

The NM_002851.3(PTPRZ1):​c.58+15224T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,956 control chromosomes in the GnomAD database, including 22,902 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 0.54 (22902 hom., cov: 32)
• Consequence: PTPRZ1 NM_002851.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

Genes affected

PTPRZ1 (HGNC:9685): (protein tyrosine phosphatase receptor type Z1) This gene encodes a member of the receptor protein tyrosine phosphatase family. Expression of this gene is restricted to the central nervous system (CNS), and it may be involved in the regulation of specific developmental processes in the CNS. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, May 2011]

PTPRZ1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPRZ1	NM_002851.3	c.58+15224T>C		intron_variant		ENST00000393386.7	NP_002842.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPRZ1	ENST00000393386.7	c.58+15224T>C		intron_variant		1	NM_002851.3	ENSP00000377047.2

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82195 AN: 151840 Hom.: 22870 Cov.: 32

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.541 AC: 82282 AN: 151956 Hom.: 22902 Cov.: 32 AF XY: 0.543 AC XY: 40364 AN XY: 74290

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.503

Alfa AF: 0.533 Hom.: 2750

Bravo AF: 0.545

Asia WGS AF: 0.601 AC: 2072 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.68

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: rs1916889; hg19: chr7-121528835;