10-118039423-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_014904.3(RAB11FIP2):​c.814C>T​(p.His272Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,611,418 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000092 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000045 ( 0 hom. )

Consequence

RAB11FIP2
NM_014904.3 missense

Scores

2
13
4

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.27
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2523306).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RAB11FIP2NM_014904.3 linkuse as main transcriptc.814C>T p.His272Tyr missense_variant 3/5 ENST00000355624.8 NP_055719.1
RAB11FIP2NM_001330167.2 linkuse as main transcriptc.814C>T p.His272Tyr missense_variant 3/6 NP_001317096.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RAB11FIP2ENST00000355624.8 linkuse as main transcriptc.814C>T p.His272Tyr missense_variant 3/51 NM_014904.3 ENSP00000347839 P1Q7L804-1
RAB11FIP2ENST00000369199.5 linkuse as main transcriptc.814C>T p.His272Tyr missense_variant 3/61 ENSP00000358200 Q7L804-2
ENST00000451610.6 linkuse as main transcriptn.164-723G>A intron_variant, non_coding_transcript_variant 2
RAB11FIP2ENST00000483413.1 linkuse as main transcriptn.208C>T non_coding_transcript_exon_variant 2/22

Frequencies

GnomAD3 genomes
AF:
0.0000921
AC:
14
AN:
152076
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000162
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.0000562
AC:
14
AN:
249310
Hom.:
0
AF XY:
0.0000594
AC XY:
8
AN XY:
134766
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000116
Gnomad OTH exome
AF:
0.000165
GnomAD4 exome
AF:
0.0000452
AC:
66
AN:
1459224
Hom.:
0
Cov.:
30
AF XY:
0.0000455
AC XY:
33
AN XY:
725740
show subpopulations
Gnomad4 AFR exome
AF:
0.0000300
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000540
Gnomad4 OTH exome
AF:
0.0000498
GnomAD4 genome
AF:
0.0000920
AC:
14
AN:
152194
Hom.:
0
Cov.:
32
AF XY:
0.0000941
AC XY:
7
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000162
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.000155
Hom.:
0
Bravo
AF:
0.0000831
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.0000824
AC:
10
EpiCase
AF:
0.000109
EpiControl
AF:
0.00

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsAug 10, 2023The c.814C>T (p.H272Y) alteration is located in exon 3 (coding exon 3) of the RAB11FIP2 gene. This alteration results from a C to T substitution at nucleotide position 814, causing the histidine (H) at amino acid position 272 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.35
BayesDel_addAF
Uncertain
0.031
T
BayesDel_noAF
Uncertain
0.010
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Benign
0.30
T;.
Eigen
Uncertain
0.62
Eigen_PC
Uncertain
0.66
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Uncertain
0.91
D;D
M_CAP
Benign
0.027
D
MetaRNN
Benign
0.25
T;T
MetaSVM
Uncertain
-0.23
T
MutationAssessor
Pathogenic
3.1
M;M
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.61
T
PROVEAN
Uncertain
-3.9
D;D
REVEL
Uncertain
0.40
Sift
Uncertain
0.0010
D;D
Sift4G
Uncertain
0.042
D;T
Polyphen
0.61
P;.
Vest4
0.67
MVP
0.39
MPC
0.15
ClinPred
0.45
T
GERP RS
5.8
Varity_R
0.69
gMVP
0.60

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs184218805; hg19: chr10-119798934; API