rs72344675
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chr2-73081095-TTCCTCCTCCTCCTCCTCCTCCTCC-T
- chr2-73081095-TTCCTCCTCCTCCTCCTCCTCCTCC-TTCCTCC
- chr2-73081095-TTCCTCCTCCTCCTCCTCCTCCTCC-TTCCTCCTCC
- chr2-73081095-TTCCTCCTCCTCCTCCTCCTCCTCC-TTCCTCCTCCTCC
- chr2-73081095-TTCCTCCTCCTCCTCCTCCTCCTCC-TTCCTCCTCCTCCTCC
- chr2-73081095-TTCCTCCTCCTCCTCCTCCTCCTCC-TTCCTCCTCCTCCTCCTCC
- chr2-73081095-TTCCTCCTCCTCCTCCTCCTCCTCC-TTCCTCCTCCTCCTCCTCCTCC
- chr2-73081095-TTCCTCCTCCTCCTCCTCCTCCTCC-TTCCTCCTCCTCCTCCTCCTCCTCCTCC
- chr2-73081095-TTCCTCCTCCTCCTCCTCCTCCTCC-TTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC
- chr2-73081095-TTCCTCCTCCTCCTCCTCCTCCTCC-TTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC
- chr2-73081095-TTCCTCCTCCTCCTCCTCCTCCTCC-TTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC
- chr2-73081095-TTCCTCCTCCTCCTCCTCCTCCTCC-TTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3
The NM_001371272.1(RAB11FIP5):c.2113_2136delGGAGGAGGAGGAGGAGGAGGAGGA(p.Gly705_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 0.00000244 in 1,229,804 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 0)
Exomes 𝑓: 9.3e-7 ( 0 hom. )
Consequence
RAB11FIP5
NM_001371272.1 conservative_inframe_deletion
NM_001371272.1 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.12
Publications
1 publications found
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]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001371272.1
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| RAB11FIP5 | NM_001371272.1 | c.2113_2136delGGAGGAGGAGGAGGAGGAGGAGGA | p.Gly705_Gly712del | conservative_inframe_deletion | Exon 4 of 6 | ENST00000486777.7 | NP_001358201.1 | |
| RAB11FIP5 | NM_015470.3 | c.1569-4937_1569-4914delGGAGGAGGAGGAGGAGGAGGAGGA | intron_variant | Intron 3 of 4 | NP_056285.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| RAB11FIP5 | ENST00000486777.7 | c.2113_2136delGGAGGAGGAGGAGGAGGAGGAGGA | p.Gly705_Gly712del | conservative_inframe_deletion | Exon 4 of 6 | 5 | NM_001371272.1 | ENSP00000489752.1 |
Frequencies
GnomAD3 genomes 0.0000134 AC: 2AN: 149636Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
149636
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 9.26e-7 AC: 1AN: 1080168Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 510580 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1
AN:
1080168
Hom.:
AF XY:
AC XY:
0
AN XY:
510580
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
22776
American (AMR)
AF:
AC:
0
AN:
8438
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
14386
East Asian (EAS)
AF:
AC:
0
AN:
26490
South Asian (SAS)
AF:
AC:
1
AN:
19508
European-Finnish (FIN)
AF:
AC:
0
AN:
21534
Middle Eastern (MID)
AF:
AC:
0
AN:
2954
European-Non Finnish (NFE)
AF:
AC:
0
AN:
920352
Other (OTH)
AF:
AC:
0
AN:
43730
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.275
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0000134 AC: 2AN: 149636Hom.: 0 Cov.: 0 AF XY: 0.0000274 AC XY: 2AN XY: 72980 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
149636
Hom.:
Cov.:
0
AF XY:
AC XY:
2
AN XY:
72980
show subpopulations
African (AFR)
AF:
AC:
0
AN:
40700
American (AMR)
AF:
AC:
0
AN:
15084
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3442
East Asian (EAS)
AF:
AC:
0
AN:
4988
South Asian (SAS)
AF:
AC:
1
AN:
4726
European-Finnish (FIN)
AF:
AC:
0
AN:
10344
Middle Eastern (MID)
AF:
AC:
0
AN:
312
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67094
Other (OTH)
AF:
AC:
0
AN:
2046
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.550
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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