chr11-18771813-T-G

Variant names:

• chr11-18771813-T-G
• rs4075664
• NM_006906.2:c.20+126A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006906.2(PTPN5):​c.20+126A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PTPN5 NM_006906.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

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.20+126A>C		intron	N/A	NP_008837.1
	PTPN5	NM_032781.4		c.20+126A>C		intron	N/A	NP_116170.3
	PTPN5	NM_001278238.2		c.-52-5930A>C		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.20+126A>C		intron	N/A	ENSP00000351342.2
	PTPN5	ENST00000396168.1	TSL:1	c.-52-5930A>C		intron	N/A	ENSP00000379471.1
	PTPN5	ENST00000396170.5	TSL:2	c.20+126A>C		intron	N/A	ENSP00000379473.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 639924 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 343834

African (AFR) AF: 0.00 AC: 0 AN: 14016

American (AMR) AF: 0.00 AC: 0 AN: 25168

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18658

East Asian (EAS) AF: 0.00 AC: 0 AN: 30580

South Asian (SAS) AF: 0.00 AC: 0 AN: 55666

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51298

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2924

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 408862

Other (OTH) AF: 0.00 AC: 0 AN: 32752

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.60
DANN	Benign	0.54
PhyloP100		-0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs4075664; hg19: chr11-18793360;