dbSNP rs2038227: RAB11FIP3:c.1265+140C>A (chr16-489140-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

18 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014700.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RAB11FIP3	NM_014700.4	MANE Select	c.1265+140C>A	intron	N/A	NP_055515.1	O75154-1
RAB11FIP3	NM_001370401.1		c.1265+140C>A	intron	N/A	NP_001357330.1	O75154-3
RAB11FIP3	NM_001142272.2		c.335+140C>A	intron	N/A	NP_001135744.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RAB11FIP3	ENST00000262305.9	TSL:1 MANE Select	c.1265+140C>A	intron	N/A	ENSP00000262305.4	O75154-1
RAB11FIP3	ENST00000941645.1		c.1265+140C>A	intron	N/A	ENSP00000611704.1
RAB11FIP3	ENST00000941647.1		c.1406+140C>A	intron	N/A	ENSP00000611706.1

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

African (AFR)

AF:

0.719

AC:

14109

AN:

19612

American (AMR)

AF:

0.466

AC:

7484

AN:

16056

Ashkenazi Jewish (ASJ)

AF:

0.592

AC:

9197

AN:

15540

East Asian (EAS)

AF:

0.490

AC:

14698

AN:

30024

South Asian (SAS)

AF:

0.412

AC:

20332

AN:

49298

European-Finnish (FIN)

AF:

0.616

AC:

18953

AN:

30780

Middle Eastern (MID)

AF:

0.661

AC:

2188

AN:

3312

European-Non Finnish (NFE)

AF:

0.604

AC:

417196

AN:

690616

Other (OTH)

AF:

0.592

AC:

23354

AN:

39468

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

10188

20375

30563

40750

50938

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10542

21084

31626

42168

52710

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.614

AC:

93302

AN:

152018

Hom.:

29023

Cov.:

AF XY:

0.607

AC XY:

45067

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.706

AC:

29283

AN:

41452

American (AMR)

AF:

0.514

AC:

7854

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.610

AC:

2115

AN:

3470

East Asian (EAS)

AF:

0.472

AC:

2437

AN:

5166

South Asian (SAS)

AF:

0.424

AC:

2045

AN:

4820

European-Finnish (FIN)

AF:

0.607

AC:

6407

AN:

10560

Middle Eastern (MID)

AF:

0.680

AC:

200

AN:

294

European-Non Finnish (NFE)

AF:

0.605

AC:

41108

AN:

67958

Other (OTH)

AF:

0.612

AC:

1293

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1834

3667

5501

7334

9168

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

764

1528

2292

3056

3820

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.601

Hom.:

47880

Bravo

AF:

0.615

Asia WGS

AF:

0.529

AC:

1843

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.61

(source)

DANN

Benign

0.51

PhyloP100

-0.18

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over