Genetic Variant RAB11FIP2:c.1266-3014G>A (chr10-118018124-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014904.3(RAB11FIP2):c.1266-3014G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0743 in 152,278 control chromosomes in the GnomAD database, including 759 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 0.074 ( 759 hom., cov: 33)

Exomes 𝑓: 0.063 ( 0 hom. )

Consequence

RAB11FIP2
NM_014904.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.06

Publications

1 publications found

Variant links:

Genes affected

RAB11FIP2 (HGNC:29152): (RAB11 family interacting protein 2) Enables protein homodimerization activity and protein kinase binding activity. Involved in several processes, including TRAM-dependent toll-like receptor 4 signaling pathway; phagocytosis; and positive regulation of GTPase activity. Located in endosome; nucleoplasm; and phagocytic cup. [provided by Alliance of Genome Resources, Apr 2022]

RAB11FIP2 links:

ENSG00000231104 (HGNC:):

ENSG00000231104 links:

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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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB11FIP2	NM_014904.3 link	c.1266-3014G>A		intron_variant	Intron 3 of 4	ENST00000355624.8	NP_055719.1	Q7L804-1
RAB11FIP2	NM_001330167.2 link	c.1326-3014G>A		intron_variant	Intron 4 of 5		NP_001317096.1	Q7L804-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
RAB11FIP2	ENST00000355624.8 link	c.1266-3014G>A	intron_variant	Intron 3 of 4	1	NM_014904.3	ENSP00000347839.3	Q7L804-1
RAB11FIP2	ENST00000369199.5 link	c.1326-3014G>A	intron_variant	Intron 4 of 5	1		ENSP00000358200.3	Q7L804-2
ENSG00000231104	ENST00000595446.1 link	n.606C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000231104	ENST00000451610.6 link	n.163+475C>T	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.0743

AC:

11307

AN:

152144

Hom.:

758

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0838

Gnomad AMI

AF:

0.0308

Gnomad AMR

AF:

0.102

Gnomad ASJ

AF:

0.0991

Gnomad EAS

AF:

0.403

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.0802

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0342

Gnomad OTH

AF:

0.0617

GnomAD4 exome

AF:

0.0625

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0625

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0833

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0743

AC:

11314

AN:

152262

Hom.:

759

Cov.:

AF XY:

0.0804

AC XY:

5983

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.0836

AC:

3474

AN:

41550

American (AMR)

AF:

0.102

AC:

1567

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0991

AC:

344

AN:

3472

East Asian (EAS)

AF:

0.403

AC:

2083

AN:

5174

South Asian (SAS)

AF:

0.105

AC:

505

AN:

4816

European-Finnish (FIN)

AF:

0.0802

AC:

850

AN:

10602

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0342

AC:

2326

AN:

68036

Other (OTH)

AF:

0.0611

AC:

129

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

506

1012

1517

2023

2529

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

272

408

544

680

<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:

0.0544

Hom.:

Bravo

AF:

0.0787

Asia WGS

AF:

0.239

AC:

828

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

(source)

DANN

Benign

0.54

PhyloP100

2.1

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over