Variant rs28362491 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000563833.1(ENSG00000260651):n.319_322del variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 153,546 control chromosomes in the GnomAD database, including 14,272 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.43 ( 14166 hom., cov: 0)

Exomes 𝑓: 0.32 ( 106 hom. )

Consequence

ENST00000563833.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0720

Variant links:

Genes affected

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377621	NR_136202.1 linkuse as main transcript	n.48+1438_48+1441del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000563833.1 linkuse as main transcript	n.319_322del		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.428

AC:

64938

AN:

151662

Hom.:

14138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.494

Gnomad AMI

AF:

0.359

Gnomad AMR

AF:

0.484

Gnomad ASJ

AF:

0.333

Gnomad EAS

AF:

0.402

Gnomad SAS

AF:

0.298

Gnomad FIN

AF:

0.447

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.391

Gnomad OTH

AF:

0.402

GnomAD4 exome

AF:

0.323

AC:

570

AN:

1764

Hom.:

106

AF XY:

0.327

AC XY:

353

AN XY:

1080

show subpopulations

Gnomad4 AFR exome

AF:

0.350

Gnomad4 AMR exome

AF:

0.429

Gnomad4 ASJ exome

AF:

0.139

Gnomad4 EAS exome

AF:

0.313

Gnomad4 SAS exome

AF:

0.167

Gnomad4 FIN exome

AF:

0.489

Gnomad4 NFE exome

AF:

0.331

Gnomad4 OTH exome

AF:

0.256

GnomAD4 genome

AF:

0.428

AC:

65010

AN:

151782

Hom.:

14166

Cov.:

AF XY:

0.429

AC XY:

31815

AN XY:

74188

show subpopulations

Gnomad4 AFR

AF:

0.494

Gnomad4 AMR

AF:

0.485

Gnomad4 ASJ

AF:

0.333

Gnomad4 EAS

AF:

0.403

Gnomad4 SAS

AF:

0.297

Gnomad4 FIN

AF:

0.447

Gnomad4 NFE

AF:

0.391

Gnomad4 OTH

AF:

0.398

Alfa

AF:

0.416

Hom.:

1645

Bravo

AF:

0.439

Asia WGS

AF:

0.354

AC:

1226

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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