15-75463126-C-T

Variant names:

• chr15-75463126-C-T
• rs4886707
• NM_002833.4:c.*5643G>A

Variant summary

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

The NM_002833.4(PTPN9):​c.*5643G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,094 control chromosomes in the GnomAD database, including 9,173 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 0.33 (9169 hom., cov: 31)
  • Exomes 𝑓: 0.25 (4 hom.)
• Consequence: PTPN9 NM_002833.4 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 45 publications found

Genes affected

PTPN9 (HGNC:9661): (protein tyrosine phosphatase non-receptor type 9) 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 N-terminal domain that shares a significant similarity with yeast SEC14, which is a protein that has phosphatidylinositol transfer activity and is required for protein secretion through the Golgi complex in yeast. This PTP was found to be activated by polyphosphoinositide, and is thought to be involved in signaling events regulating phagocytosis. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002833.4. 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
	PTPN9	NM_002833.4	MANE Select	c.*5643G>A		downstream_gene	N/A	NP_002824.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPN9	ENST00000618819.5	TSL:1 MANE Select	c.*5643G>A		downstream_gene	N/A	ENSP00000482732.1

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50114 AN: 151846 Hom.: 9148 Cov.: 31

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.353

GnomAD4 exome AF: 0.246 AC: 32 AN: 130 Hom.: 4 AF XY: 0.271 AC XY: 26 AN XY: 96

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.333 AC: 2 AN: 6

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.231 AC: 6 AN: 26

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.239 AC: 21 AN: 88

Other (OTH) AF: 0.167 AC: 1 AN: 6

GnomAD4 genome AF: 0.330 AC: 50179 AN: 151964 Hom.: 9169 Cov.: 31 AF XY: 0.330 AC XY: 24540 AN XY: 74290

African (AFR) AF: 0.472 AC: 19537 AN: 41412

American (AMR) AF: 0.287 AC: 4383 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1326 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1785 AN: 5174

South Asian (SAS) AF: 0.413 AC: 1986 AN: 4814

European-Finnish (FIN) AF: 0.207 AC: 2191 AN: 10562

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17771 AN: 67972

Other (OTH) AF: 0.357 AC: 753 AN: 2108

Alfa AF: 0.291 Hom.: 21248

Bravo AF: 0.338

Asia WGS AF: 0.379 AC: 1314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs4886707; hg19: chr15-75755467;