9-8331574-A-AAACTTACCATTCTTGAACTGT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_002839.4(PTPRD):c.5534+7_5534+8insACAGTTCAAGAATGGTAAGTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 1,605,656 control chromosomes in the GnomAD database, including 37,338 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.30 (10516 hom., cov: 0)
  • Exomes 𝑓: 0.17 (26822 hom.)
• Consequence: PTPRD NM_002839.4 splice_region, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.111

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 -10 ACMG points.

• BP6: Variant 9-8331574-A-AAACTTACCATTCTTGAACTGT is Benign according to our data. Variant chr9-8331574-A-AAACTTACCATTCTTGAACTGT is described in ClinVar as [Likely_benign]. Clinvar id is 1317827.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRD	NM_002839.4	c.5534+7_5534+8insACAGTTCAAGAATGGTAAGTT		splice_region_variant, intron_variant		ENST00000381196.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRD	ENST00000381196.9	c.5534+7_5534+8insACAGTTCAAGAATGGTAAGTT		splice_region_variant, intron_variant		5	NM_002839.4	P1

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44911 AN: 151838 Hom.: 10494 Cov.: 0

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.278

GnomAD4 exome AF: 0.170 AC: 246601 AN: 1453702 Hom.: 26822 Cov.: 35 AF XY: 0.170 AC XY: 122778 AN XY: 723430

Gnomad4 AFR exome AF: 0.678

Gnomad4 AMR exome AF: 0.130

Gnomad4 ASJ exome AF: 0.255

Gnomad4 EAS exome AF: 0.147

Gnomad4 SAS exome AF: 0.198

Gnomad4 FIN exome AF: 0.107

Gnomad4 NFE exome AF: 0.154

Gnomad4 OTH exome AF: 0.188

GnomAD4 genome AF: 0.296 AC: 44987 AN: 151954 Hom.: 10516 Cov.: 0 AF XY: 0.288 AC XY: 21389 AN XY: 74286

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.278

Alfa AF: 0.136 Hom.: 255

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3215098; hg19: chr9-8331574;