Genetic Variant RAB11FIP5:p.Gly711_Gly712del (chr2-73081095-TTCCTCC-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP3BP6_ModerateBA1

The NM_001371272.1(RAB11FIP5):c.2131_2136delGGAGGA(p.Gly711_Gly712del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 1,229,726 control chromosomes in the GnomAD database, including 38,519 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.32 ( 8797 hom., cov: 0)

Exomes 𝑓: 0.23 ( 29722 hom. )

Consequence

RAB11FIP5
NM_001371272.1 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.12

Publications

1 publications found

Variant links:

Genes affected

RAB11FIP5 (HGNC:24845): (RAB11 family interacting protein 5) Enables gamma-tubulin binding activity. Involved in cellular response to acidic pH; negative regulation of adiponectin secretion; and regulation of protein localization to cell surface. Located in centriolar satellite and mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]

RAB11FIP5 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001371272.1

BP6

Variant 2-73081095-TTCCTCC-T is Benign according to our data. Variant chr2-73081095-TTCCTCC-T is described in ClinVar as [Benign]. Clinvar id is 3910193.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB11FIP5	NM_001371272.1 link	c.2131_2136delGGAGGA	p.Gly711_Gly712del	conservative_inframe_deletion	Exon 4 of 6	ENST00000486777.7	NP_001358201.1
RAB11FIP5	NM_015470.3 link	c.1569-4919_1569-4914delGGAGGA		intron_variant	Intron 3 of 4		NP_056285.1	Q9BXF6Q9UFM0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB11FIP5	ENST00000486777.7 link	c.2131_2136delGGAGGA	p.Gly711_Gly712del	conservative_inframe_deletion	Exon 4 of 6	5	NM_001371272.1	ENSP00000489752.1		A0A1B0GTL5

Frequencies

GnomAD3 genomes

AF:

0.317

AC:

47410

AN:

149526

Hom.:

8788

Cov.:

show subpopulations

Gnomad AFR

AF:

0.504

Gnomad AMI

AF:

0.196

Gnomad AMR

AF:

0.264

Gnomad ASJ

AF:

0.265

Gnomad EAS

AF:

0.550

Gnomad SAS

AF:

0.290

Gnomad FIN

AF:

0.273

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.213

Gnomad OTH

AF:

0.292

GnomAD4 exome

AF:

0.229

AC:

247216

AN:

1080096

Hom.:

29722

AF XY:

0.228

AC XY:

116222

AN XY:

510550

show subpopulations

African (AFR)

AF:

0.511

AC:

11643

AN:

22770

American (AMR)

AF:

0.268

AC:

2263

AN:

8438

Ashkenazi Jewish (ASJ)

AF:

0.271

AC:

3893

AN:

14386

East Asian (EAS)

AF:

0.577

AC:

15290

AN:

26486

South Asian (SAS)

AF:

0.284

AC:

5545

AN:

19504

European-Finnish (FIN)

AF:

0.254

AC:

5476

AN:

21534

Middle Eastern (MID)

AF:

0.219

AC:

647

AN:

2954

European-Non Finnish (NFE)

AF:

0.208

AC:

191077

AN:

920298

Other (OTH)

AF:

0.260

AC:

11382

AN:

43726

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

11741

23482

35223

46964

58705

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.317

AC:

47462

AN:

149630

Hom.:

8797

Cov.:

AF XY:

0.320

AC XY:

23375

AN XY:

73036

show subpopulations

African (AFR)

AF:

0.504

AC:

20541

AN:

40762

American (AMR)

AF:

0.264

AC:

3980

AN:

15090

Ashkenazi Jewish (ASJ)

AF:

0.265

AC:

910

AN:

3438

East Asian (EAS)

AF:

0.549

AC:

2731

AN:

4972

South Asian (SAS)

AF:

0.292

AC:

1375

AN:

4710

European-Finnish (FIN)

AF:

0.273

AC:

2823

AN:

10340

Middle Eastern (MID)

AF:

0.238

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.213

AC:

14256

AN:

67062

Other (OTH)

AF:

0.291

AC:

601

AN:

2066

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1454

2907

4361

5814

7268

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0725

Hom.:

103

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Feb 16, 2025

Laboratory of Genetics, Children's Clinical University Hospital Latvia

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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2-73081095-TTCCTCC-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over