Genetic Variant RAB11FIP5:p.Gly712dup (chr2-73081095-T-TTCC) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP3BS2

The NM_001371272.1(RAB11FIP5):c.2134_2136dupGGA(p.Gly712dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0033 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0032 ( 6 hom. )

Consequence

RAB11FIP5
NM_001371272.1 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0420

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001371272.1

BS2

High Homozygotes in GnomAdExome4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB11FIP5	NM_001371272.1 link	c.2134_2136dupGGA	p.Gly712dup	conservative_inframe_insertion	Exon 4 of 6	ENST00000486777.7	NP_001358201.1
RAB11FIP5	NM_015470.3 link	c.1569-4916_1569-4914dupGGA		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.2134_2136dupGGA	p.Gly712dup	conservative_inframe_insertion	Exon 4 of 6	5	NM_001371272.1	ENSP00000489752.1		A0A1B0GTL5

Frequencies

GnomAD3 genomes

AF:

0.00327

AC:

490

AN:

149632

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00351

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00265

Gnomad ASJ

AF:

0.00233

Gnomad EAS

AF:

0.00401

Gnomad SAS

AF:

0.00868

Gnomad FIN

AF:

0.00174

Gnomad MID

AF:

0.00641

Gnomad NFE

AF:

0.00313

Gnomad OTH

AF:

0.00391

GnomAD4 exome

AF:

0.00318

AC:

3430

AN:

1080156

Hom.:

Cov.:

AF XY:

0.00323

AC XY:

1651

AN XY:

510578

show subpopulations

African (AFR)

AF:

0.00373

AC:

AN:

22776

American (AMR)

AF:

0.00261

AC:

AN:

8438

Ashkenazi Jewish (ASJ)

AF:

0.00202

AC:

AN:

14386

East Asian (EAS)

AF:

0.00419

AC:

111

AN:

26490

South Asian (SAS)

AF:

0.0114

AC:

222

AN:

19508

European-Finnish (FIN)

AF:

0.00130

AC:

AN:

21534

Middle Eastern (MID)

AF:

0.0179

AC:

AN:

2954

European-Non Finnish (NFE)

AF:

0.00293

AC:

2701

AN:

920342

Other (OTH)

AF:

0.00409

AC:

179

AN:

43728

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.454

Heterozygous variant carriers

217

434

650

867

1084

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00327

AC:

489

AN:

149734

Hom.:

Cov.:

AF XY:

0.00309

AC XY:

226

AN XY:

73090

show subpopulations

African (AFR)

AF:

0.00348

AC:

142

AN:

40812

American (AMR)

AF:

0.00265

AC:

AN:

15104

Ashkenazi Jewish (ASJ)

AF:

0.00233

AC:

AN:

3440

East Asian (EAS)

AF:

0.00402

AC:

AN:

4976

South Asian (SAS)

AF:

0.00869

AC:

AN:

4716

European-Finnish (FIN)

AF:

0.00174

AC:

AN:

10344

Middle Eastern (MID)

AF:

0.00690

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.00313

AC:

210

AN:

67086

Other (OTH)

AF:

0.00387

AC:

AN:

2066

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

101

126

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00120

Hom.:

103

Bravo

AF:

0.00304

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.042

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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.

2-73081095-TTCCTCCTCCTCCTCCTCCTCCTCC-TTCCTCCTCCTCCTCCTCCTCCTCCTCC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over