rs1092535

Variant names:

• chr10-48092954-T-A
• rs1092535
• ENST00000614090.1:n.464-6089A>T

Your query was ambiguous. Multiple possible variants found:

• chr10-48092954-T-A
• chr10-48092954-T-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000614090.1(PTPN20CP):​n.464-6089A>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.18
• Publications: 1 publications found

Genes affected

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

ENSG00000289444 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPN20CP	ENST00000614090.1	n.464-6089A>T		intron_variant	Intron 4 of 6	6
ENSG00000289444	ENST00000687180.1	n.299-6089A>T		intron_variant	Intron 3 of 14
ENSG00000289143	ENST00000687926.1	n.264-6089A>T		intron_variant	Intron 2 of 19

Frequencies

GnomAD3 genomes AF: 0.289 AC: 17299 AN: 59892 Hom.: 1663 Cov.: 10

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.291 AC: 4993 AN: 17132

American (AMR) AF: 0.251 AC: 1672 AN: 6662

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 442 AN: 1390

East Asian (EAS) AF: 0.319 AC: 495 AN: 1550

South Asian (SAS) AF: 0.166 AC: 382 AN: 2298

European-Finnish (FIN) AF: 0.291 AC: 1090 AN: 3748

Middle Eastern (MID) AF: 0.221 AC: 23 AN: 104

European-Non Finnish (NFE) AF: 0.305 AC: 7900 AN: 25922

Other (OTH) AF: 0.253 AC: 197 AN: 780

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs1092535; hg19: chr10-49300997;