9-9800624-T-C

Variant names:

• chr9-9800624-T-C
• rs1746799
• NM_002839.4:c.-367-33773A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002839.4(PTPRD):​c.-367-33773A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,130 control chromosomes in the GnomAD database, including 33,354 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 0.64 (33354 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 4 publications found

Genes affected

PTPRD (HGNC:9668): (protein tyrosine phosphatase receptor type D) The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP contains an extracellular region, a single transmembrane segment and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. The extracellular region of this protein is composed of three Ig-like and eight fibronectin type III-like domains. Studies of the similar genes in chicken and fly suggest the role of this PTP is in promoting neurite growth, and regulating neurons axon guidance. Multiple alternatively spliced transcript variants of this gene have been reported. A related pseudogene has been identified on chromosome 5. [provided by RefSeq, Jan 2010]

ENSG00000230920 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002839.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRD	NM_002839.4	MANE Select	c.-367-33773A>G		intron	N/A	NP_002830.1	P23468-1
	LOC105375972	NR_135135.1		n.296T>C		non_coding_transcript_exon	Exon 2 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRD	ENST00000381196.9	TSL:5 MANE Select	c.-367-33773A>G		intron	N/A	ENSP00000370593.3	P23468-1
	PTPRD	ENST00000463477.5	TSL:1	c.-439-33773A>G		intron	N/A	ENSP00000417661.1	C9J8S8
	PTPRD	ENST00000850942.1		c.-367-33773A>G		intron	N/A	ENSP00000521027.1

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97567 AN: 152012 Hom.: 33286 Cov.: 33

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.593

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.642 AC: 97696 AN: 152130 Hom.: 33354 Cov.: 33 AF XY: 0.644 AC XY: 47896 AN XY: 74362

African (AFR) AF: 0.871 AC: 36197 AN: 41548

American (AMR) AF: 0.664 AC: 10137 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1704 AN: 3466

East Asian (EAS) AF: 0.872 AC: 4508 AN: 5170

South Asian (SAS) AF: 0.536 AC: 2590 AN: 4828

European-Finnish (FIN) AF: 0.544 AC: 5759 AN: 10588

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34785 AN: 67946

Other (OTH) AF: 0.598 AC: 1261 AN: 2110

Alfa AF: 0.553 Hom.: 72818

Bravo AF: 0.666

Asia WGS AF: 0.744 AC: 2587 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.75
DANN	Benign	0.58
PhyloP100		-1.3
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: rs1746799; hg19: chr9-9800624;