NM_006906.2:c.97+3567C>T

Variant names:

• chr11-18762240-G-A
• rs11024787
• NM_006906.2:c.97+3567C>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.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
• 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]

ENSG00000286998 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PTPN5	NM_006906.2	c.97+3567C>T		intron_variant	Intron 3 of 14	ENST00000358540.7	NP_008837.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPN5	ENST00000358540.7	c.97+3567C>T		intron_variant	Intron 3 of 14	1	NM_006906.2	ENSP00000351342.2
PTPN5	ENST00000396168.1	c.25+3567C>T		intron_variant	Intron 2 of 13	1		ENSP00000379471.1
PTPN5	ENST00000396170.5	c.97+3567C>T		intron_variant	Intron 3 of 14	2		ENSP00000379473.1
ENSG00000286998	ENST00000657264.1	n.183+394G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.334 AC: 13851 AN: 41478

American (AMR) AF: 0.155 AC: 2374 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 366 AN: 3472

East Asian (EAS) AF: 0.0391 AC: 202 AN: 5166

South Asian (SAS) AF: 0.0925 AC: 446 AN: 4824

European-Finnish (FIN) AF: 0.297 AC: 3139 AN: 10586

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16638 AN: 67956

Other (OTH) AF: 0.196 AC: 414 AN: 2112

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
PhyloP100		0.093
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: rs11024787; hg19: chr11-18783787;