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GeneBe

rs2038227

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

2

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]

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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 UniProt
RAB11FIP3NM_014700.4 linkuse as main transcriptc.1265+140C>A intron_variant ENST00000262305.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RAB11FIP3ENST00000262305.9 linkuse as main transcriptc.1265+140C>A intron_variant 1 NM_014700.4 O75154-1

Frequencies

GnomAD3 genomes
AF:
0.614
AC:
93241
AN:
151900
Hom.:
29008
Cov.:
33
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.:
11
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.:
33
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.

Other links and lift over

dbSNP: rs2038227; hg19: chr16-539140; COSMIC: COSV51932036; COSMIC: COSV51932036; API