9-8331574-A-AAACTTACTTACCATTCTTGAACTGT

Position:

• chr9-8331574-A-AAACTTACTTACCATTCTTGAACTGT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_002839.4(PTPRD):​c.5534+7_5534+8insACAGTTCAAGAATGGTAAGTAAGTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.013 (42 hom., cov: 0)
  • Exomes 𝑓: 0.0014 (56 hom.)
  • Failed GnomAD Quality Control
• 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-AAACTTACTTACCATTCTTGAACTGT is Benign according to our data. Variant chr9-8331574-A-AAACTTACTTACCATTCTTGAACTGT is described in ClinVar as [Likely_benign]. Clinvar id is 2504285.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0129 (1966/152024) while in subpopulation AFR AF= 0.0439 (1817/41426). AF 95% confidence interval is 0.0422. There are 42 homozygotes in gnomad4. There are 909 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 1966 AD gene.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.0129 AC: 1959 AN: 151908 Hom.: 43 Cov.: 0

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00741

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000235

Gnomad OTH AF: 0.00913

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00143 AC: 2084 AN: 1460110 Hom.: 56 Cov.: 35 AF XY: 0.00121 AC XY: 877 AN XY: 726472

Gnomad4 AFR exome AF: 0.0481

Gnomad4 AMR exome AF: 0.00379

Gnomad4 ASJ exome AF: 0.0000383

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000813

Gnomad4 FIN exome AF: 0.0000188

Gnomad4 NFE exome AF: 0.0000954

Gnomad4 OTH exome AF: 0.00302

GnomAD4 genome AF: 0.0129 AC: 1966 AN: 152024 Hom.: 42 Cov.: 0 AF XY: 0.0122 AC XY: 909 AN XY: 74316

Gnomad4 AFR AF: 0.0439

Gnomad4 AMR AF: 0.00740

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000208

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000235

Gnomad4 OTH AF: 0.00903

Alfa AF: 0.000567 Hom.: 0

Bravo AF: 0.0148

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 07, 2023

See Variant Classification Assertion Criteria. -

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: rs368394000; hg19: chr9-8331574;