Variant rs889206 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000563866.1(ENSG00000260242):n.48+49078G>A 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 0.0016 ( 0 hom., cov: 17)

Failed GnomAD Quality Control

Consequence

ENSG00000260242
ENST00000563866.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0150

Variant links:

Genes affected

ENSG00000260242 (HGNC:):

ENSG00000260242 links:

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=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000260242	ENST00000563866.1 link	n.48+49078G>A		intron_variant		3
ENSG00000259929	ENST00000567304.1 link	n.144+27514G>A		intron_variant		4

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

182

AN:

110868

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00109

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00140

Gnomad ASJ

AF:

0.000826

Gnomad EAS

AF:

0.00385

Gnomad SAS

AF:

0.00269

Gnomad FIN

AF:

0.000836

Gnomad MID

AF:

0.0250

Gnomad NFE

AF:

0.00192

Gnomad OTH

AF:

0.00141

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:

0.00165

AC:

183

AN:

110984

Hom.:

Cov.:

AF XY:

0.00146

AC XY:

AN XY:

54274

show subpopulations

Gnomad4 AFR

AF:

0.00112

Gnomad4 AMR

AF:

0.00139

Gnomad4 ASJ

AF:

0.000826

Gnomad4 EAS

AF:

0.00385

Gnomad4 SAS

AF:

0.00268

Gnomad4 FIN

AF:

0.000836

Gnomad4 NFE

AF:

0.00192

Gnomad4 OTH

AF:

0.00139

Alfa

AF:

0.0483

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.1

DANN

Benign

0.44

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over