Variant rs2038227 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014700.4(RAB11FIP3):c.1265+140C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 1,046,724 control chromosomes in the GnomAD database, including 186,856 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 0.61 ( 29023 hom., cov: 33)

Exomes 𝑓: 0.59 ( 157833 hom. )

Consequence

RAB11FIP3
NM_014700.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.180

Variant links:

Genes affected

RAB11FIP3 (HGNC:17224): (RAB11 family interacting protein 3) Proteins of the large Rab GTPase family (see RAB1A; MIM 179508) have regulatory roles in the formation, targeting, and fusion of intracellular transport vesicles. RAB11FIP3 is one of many proteins that interact with and regulate Rab GTPases (Hales et al., 2001 [PubMed 11495908]).[supplied by OMIM, Mar 2008]

RAB11FIP3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB11FIP3	NM_014700.4 linkuse as main transcript	c.1265+140C>A		intron_variant		ENST00000262305.9	NP_055515.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAB11FIP3	ENST00000262305.9 linkuse as main transcript	c.1265+140C>A		intron_variant		1	NM_014700.4	ENSP00000262305		O75154-1

Frequencies

GnomAD3 genomes

AF:

0.614

AC:

93241

AN:

151900

Hom.:

29008

Cov.:

show subpopulations

Gnomad AFR

AF:

0.706

Gnomad AMI

AF:

0.615

Gnomad AMR

AF:

0.515

Gnomad ASJ

AF:

0.610

Gnomad EAS

AF:

0.471

Gnomad SAS

AF:

0.425

Gnomad FIN

AF:

0.607

Gnomad MID

AF:

0.677

Gnomad NFE

AF:

0.605

Gnomad OTH

AF:

0.614

GnomAD4 exome

AF:

0.590

AC:

527511

AN:

894706

Hom.:

157833

Cov.:

AF XY:

0.584

AC XY:

259244

AN XY:

443936

show subpopulations

Gnomad4 AFR exome

AF:

0.719

Gnomad4 AMR exome

AF:

0.466

Gnomad4 ASJ exome

AF:

0.592

Gnomad4 EAS exome

AF:

0.490

Gnomad4 SAS exome

AF:

0.412

Gnomad4 FIN exome

AF:

0.616

Gnomad4 NFE exome

AF:

0.604

Gnomad4 OTH exome

AF:

0.592

GnomAD4 genome

AF:

0.614

AC:

93302

AN:

152018

Hom.:

29023

Cov.:

AF XY:

0.607

AC XY:

45067

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.706

Gnomad4 AMR

AF:

0.514

Gnomad4 ASJ

AF:

0.610

Gnomad4 EAS

AF:

0.472

Gnomad4 SAS

AF:

0.424

Gnomad4 FIN

AF:

0.607

Gnomad4 NFE

AF:

0.605

Gnomad4 OTH

AF:

0.612

Alfa

AF:

0.597

Hom.:

12459

Bravo

AF:

0.615

Asia WGS

AF:

0.529

AC:

1843

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.61

DANN

Benign

0.51

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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