20-3026547-T-G

Variant names:

• chr20-3026547-T-G
• rs6138982
• NM_001385305.1:c.1615-140T>G

Variant summary

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

The NM_001385305.1(PTPRA):​c.1615-140T>G 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: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PTPRA NM_001385305.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295
• Publications: 4 publications found

Genes affected

PTPRA (HGNC:9664): (protein tyrosine phosphatase receptor type A) 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 extracellular domain, a single transmembrane segment and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. This PTP has been shown to dephosphorylate and activate Src family tyrosine kinases, and is implicated in the regulation of integrin signaling, cell adhesion and proliferation. Three alternatively spliced variants of this gene, which encode two distinct isoforms, have been reported. [provided by RefSeq, Jul 2008]

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRA	NM_001385305.1	c.1615-140T>G		intron_variant	Intron 17 of 23	ENST00000399903.7	NP_001372234.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRA	ENST00000399903.7	c.1615-140T>G		intron_variant	Intron 17 of 23	5	NM_001385305.1	ENSP00000382787.2
PTPRA	ENST00000216877.10	c.1588-140T>G		intron_variant	Intron 16 of 22	1		ENSP00000216877.6
PTPRA	ENST00000356147.3	c.1588-140T>G		intron_variant	Intron 16 of 22	1		ENSP00000348468.3
PTPRA	ENST00000318266.9	c.1588-140T>G		intron_variant	Intron 17 of 23	5		ENSP00000314568.5

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 485078 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 255342

African (AFR) AF: 0.00 AC: 0 AN: 13240

American (AMR) AF: 0.00 AC: 0 AN: 22094

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14436

East Asian (EAS) AF: 0.00 AC: 0 AN: 30922

South Asian (SAS) AF: 0.00 AC: 0 AN: 46398

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40982

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3602

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 286362

Other (OTH) AF: 0.00 AC: 0 AN: 27042

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.1
DANN	Benign	0.69
PhyloP100		0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs6138982; hg19: chr20-3007193;