10-48092954-T-G

Variant summary

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

The ENST00000687180.1(ENSG00000289444):​n.299-6089A>C 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: not found (cov: 10)

Consequence

ENSG00000289444
ENST00000687180.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.18
Variant links:
Genes affected
PTPN20CP (HGNC:23424): (protein tyrosine phosphatase non-receptor type 20C, pseudogene)

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PTPN20CPENST00000614090.1 linkn.464-6089A>C intron_variant Intron 4 of 6 6
ENSG00000289444ENST00000687180.1 linkn.299-6089A>C intron_variant Intron 3 of 14
ENSG00000289143ENST00000687926.1 linkn.264-6089A>C intron_variant Intron 2 of 19

Frequencies

GnomAD3 genomes
Cov.:
10
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
10

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.24
DANN
Benign
0.31

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1092535; hg19: chr10-49300997; API