9-10043014-T-G

Position:

• chr9-10043014-T-G

Variant summary

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

The NM_002839.4(PTPRD):​c.-544-9224A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0925 in 151,922 control chromosomes in the GnomAD database, including 1,310 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 0.093 (1310 hom., cov: 32)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.745

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRD	NM_002839.4	c.-544-9224A>C		intron_variant		ENST00000381196.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRD	ENST00000381196.9	c.-544-9224A>C		intron_variant		5	NM_002839.4	P1
PTPRD	ENST00000463477.5	c.-616-9224A>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0924 AC: 14020 AN: 151804 Hom.: 1307 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0302

Gnomad FIN AF: 0.0305

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0303

Gnomad OTH AF: 0.0729

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

GnomAD4 genome AF: 0.0925 AC: 14057 AN: 151922 Hom.: 1310 Cov.: 32 AF XY: 0.0908 AC XY: 6743 AN XY: 74276

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0153

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0309

Gnomad4 FIN AF: 0.0305

Gnomad4 NFE AF: 0.0303

Gnomad4 OTH AF: 0.0722

Alfa AF: 0.0324 Hom.: 160

Bravo AF: 0.106

Asia WGS AF: 0.0260 AC: 90 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs291272; hg19: chr9-10043014;