Variant rs705698 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_002868.4(RAB5B):c.438+99T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 1,427,948 control chromosomes in the GnomAD database, including 68,954 homozygotes. 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 0.24 ( 5149 hom., cov: 32)

Exomes 𝑓: 0.31 ( 63805 hom. )

Consequence

RAB5B
NM_002868.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.25

Variant links:

Genes affected

RAB5B (HGNC:9784): (RAB5B, member RAS oncogene family) Enables GDP binding activity; GTP-dependent protein binding activity; and GTPase activity. Involved in antigen processing and presentation and plasma membrane to endosome transport. Located in endosome and extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

RAB5B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.19).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB5B	NM_002868.4 linkuse as main transcript	c.438+99T>C		intron_variant		ENST00000360299.10	NP_002859.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAB5B	ENST00000360299.10 linkuse as main transcript	c.438+99T>C		intron_variant		1	NM_002868.4	ENSP00000353444	P1	P61020-1

Frequencies

GnomAD3 genomes

AF:

0.240

AC:

36481

AN:

151984

Hom.:

5150

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0897

Gnomad AMI

AF:

0.513

Gnomad AMR

AF:

0.229

Gnomad ASJ

AF:

0.325

Gnomad EAS

AF:

0.226

Gnomad SAS

AF:

0.218

Gnomad FIN

AF:

0.286

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.321

Gnomad OTH

AF:

0.261

GnomAD4 exome

AF:

0.311

AC:

396570

AN:

1275846

Hom.:

63805

Cov.:

AF XY:

0.309

AC XY:

195558

AN XY:

633828

show subpopulations

Gnomad4 AFR exome

AF:

0.0802

Gnomad4 AMR exome

AF:

0.211

Gnomad4 ASJ exome

AF:

0.321

Gnomad4 EAS exome

AF:

0.211

Gnomad4 SAS exome

AF:

0.225

Gnomad4 FIN exome

AF:

0.295

Gnomad4 NFE exome

AF:

0.334

Gnomad4 OTH exome

AF:

0.295

GnomAD4 genome

AF:

0.240

AC:

36483

AN:

152102

Hom.:

5149

Cov.:

AF XY:

0.237

AC XY:

17585

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.0895

Gnomad4 AMR

AF:

0.229

Gnomad4 ASJ

AF:

0.325

Gnomad4 EAS

AF:

0.225

Gnomad4 SAS

AF:

0.219

Gnomad4 FIN

AF:

0.286

Gnomad4 NFE

AF:

0.321

Gnomad4 OTH

AF:

0.259

Alfa

AF:

0.255

Hom.:

1387

Bravo

AF:

0.232

Asia WGS

AF:

0.178

AC:

622

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.19

CADD

Benign

DANN

Benign

0.84

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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