rs11024787

chr11-18762240-G-Achr11-18762240-G-C

Variant summary

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

The NM_006906.2(PTPN5):c.97+3567C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,096 control chromosomes in the GnomAD database, including 5,107 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 0.25 (5107 hom., cov: 31)
• Consequence: PTPN5 NM_006906.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPN5	NM_006906.2	c.97+3567C>T		intron_variant		ENST00000358540.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPN5	ENST00000358540.7	c.97+3567C>T		intron_variant		1	NM_006906.2
PTPN5	ENST00000396168.1	c.25+3567C>T		intron_variant		1		P1
	ENST00000657264.1	n.183+394G>A		intron_variant, non_coding_transcript_variant
PTPN5	ENST00000396170.5	c.97+3567C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37524 AN: 151980 Hom.: 5103 Cov.: 31

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0390

Gnomad SAS AF: 0.0930

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.247 AC: 37563 AN: 152096 Hom.: 5107 Cov.: 31 AF XY: 0.244 AC XY: 18129 AN XY: 74344

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.0391

Gnomad4 SAS AF: 0.0925

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.196

Alfa AF: 0.170 Hom.: 491

Bravo AF: 0.239

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.1
Dann	Benign	0.72

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

Publications

LitVar

Other links and lift over

dbSNP: rs11024787; hg19: chr11-18783787;