rs10832983

Variant names:

• chr11-18766579-G-A
• rs10832983
• NM_006906.2:c.21-696C>T

Variant summary

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

The NM_006906.2(PTPN5):​c.21-696C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,090 control chromosomes in the GnomAD database, including 16,437 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 0.43 (16437 hom., cov: 33)
• Consequence: PTPN5 NM_006906.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.663
• Publications: 2 publications found

Genes affected

PTPN5 (HGNC:9657): (protein tyrosine phosphatase non-receptor type 5) Enables phosphotyrosine residue binding activity. Predicted to be involved in peptidyl-tyrosine dephosphorylation. Predicted to act upstream of or within protein dephosphorylation. Predicted to be located in nucleoplasm. Predicted to be integral component of membrane. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006906.2. 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
	PTPN5	NM_006906.2	MANE Select	c.21-696C>T		intron	N/A	NP_008837.1
	PTPN5	NM_032781.4		c.21-696C>T		intron	N/A	NP_116170.3
	PTPN5	NM_001278238.2		c.-52-696C>T		intron	N/A	NP_001265167.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPN5	ENST00000358540.7	TSL:1 MANE Select	c.21-696C>T		intron	N/A	ENSP00000351342.2
	PTPN5	ENST00000396168.1	TSL:1	c.-52-696C>T		intron	N/A	ENSP00000379471.1
	PTPN5	ENST00000935333.1		c.21-696C>T		intron	N/A	ENSP00000605392.1

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64958 AN: 151972 Hom.: 16441 Cov.: 33

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.427 AC: 64962 AN: 152090 Hom.: 16437 Cov.: 33 AF XY: 0.430 AC XY: 31961 AN XY: 74346

African (AFR) AF: 0.155 AC: 6453 AN: 41514

American (AMR) AF: 0.436 AC: 6656 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1524 AN: 3470

East Asian (EAS) AF: 0.328 AC: 1693 AN: 5162

South Asian (SAS) AF: 0.504 AC: 2422 AN: 4808

European-Finnish (FIN) AF: 0.612 AC: 6466 AN: 10572

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.562 AC: 38198 AN: 67970

Other (OTH) AF: 0.434 AC: 916 AN: 2110

Alfa AF: 0.494 Hom.: 31917

Bravo AF: 0.396

Asia WGS AF: 0.399 AC: 1389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	13
DANN	Benign	0.27
PhyloP100		0.66
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: rs10832983; hg19: chr11-18788126;