Variant rs10680577 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_037791.1(RAB4B-EGLN2):n.815-1647_815-1644dup variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.80 ( 48383 hom., cov: 0)

Consequence

RAB4B-EGLN2
NR_037791.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.811

Variant links:

Genes affected

RAB4B-EGLN2 (HGNC:):

RAB4B-EGLN2 links:

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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 = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAB4B-EGLN2	NR_037791.1 linkuse as main transcript	n.815-1647_815-1644dup		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.797

AC:

120784

AN:

151566

Hom.:

48325

Cov.:

show subpopulations

Gnomad AFR

AF:

0.839

Gnomad AMI

AF:

0.778

Gnomad AMR

AF:

0.809

Gnomad ASJ

AF:

0.787

Gnomad EAS

AF:

0.729

Gnomad SAS

AF:

0.648

Gnomad FIN

AF:

0.846

Gnomad MID

AF:

0.742

Gnomad NFE

AF:

0.778

Gnomad OTH

AF:

0.778

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

GnomAD4 genome

AF:

0.797

AC:

120906

AN:

151686

Hom.:

48383

Cov.:

AF XY:

0.796

AC XY:

59014

AN XY:

74092

show subpopulations

Gnomad4 AFR

AF:

0.839

Gnomad4 AMR

AF:

0.809

Gnomad4 ASJ

AF:

0.787

Gnomad4 EAS

AF:

0.728

Gnomad4 SAS

AF:

0.649

Gnomad4 FIN

AF:

0.846

Gnomad4 NFE

AF:

0.778

Gnomad4 OTH

AF:

0.777

Alfa

AF:

0.779

Hom.:

4922

Asia WGS

AF:

0.720

AC:

2503

AN:

3478

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