7-121888781-T-C

Variant names:

• chr7-121888781-T-C
• rs1916889
• NM_002851.3:c.58+15224T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002851.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRZ1	NM_002851.3	MANE Select	c.58+15224T>C		intron	N/A	NP_002842.2
	PTPRZ1	NM_001369395.1		c.58+15224T>C		intron	N/A	NP_001356324.1
	PTPRZ1	NM_001369396.1		c.-87-4743T>C		intron	N/A	NP_001356325.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRZ1	ENST00000393386.7	TSL:1 MANE Select	c.58+15224T>C		intron	N/A	ENSP00000377047.2
	PTPRZ1	ENST00000449182.1	TSL:1	c.58+15224T>C		intron	N/A	ENSP00000410000.1
	PTPRZ1	ENST00000651863.1		c.58+15224T>C		intron	N/A	ENSP00000498439.1

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

African (AFR) AF: 0.658 AC: 27255 AN: 41446

American (AMR) AF: 0.503 AC: 7674 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1885 AN: 3472

East Asian (EAS) AF: 0.641 AC: 3316 AN: 5174

South Asian (SAS) AF: 0.607 AC: 2921 AN: 4814

European-Finnish (FIN) AF: 0.441 AC: 4659 AN: 10560

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33024 AN: 67920

Other (OTH) AF: 0.503 AC: 1060 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.68
PhyloP100		-0.048
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1916889; hg19: chr7-121528835;