rs1092535

chr10-48092954-T-Achr10-48092954-T-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000614090.1(PTPN20CP):n.464-6089A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.29 (1663 hom., cov: 10)
  • Failed GnomAD Quality Control
• Consequence: PTPN20CP ENST00000614090.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.18

Genes affected

PTPN20CP (HGNC:23424): (protein tyrosine phosphatase non-receptor type 20C, pseudogene)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPN20CP	ENST00000614090.1	n.464-6089A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 17299 AN: 59892 Hom.: 1663 Cov.: 10 FAILED QC

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.257

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.289 AC: 17306 AN: 59954 Hom.: 1663 Cov.: 10 AF XY: 0.288 AC XY: 8488 AN XY: 29502

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.253

Alfa AF: 0.171 Hom.: 240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.23
Dann	Benign	0.22

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1092535; hg19: chr10-49300997;