10-118043804-C-T

Position:

• chr10-118043804-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014904.3(RAB11FIP2):​c.353+2007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.099 in 152,110 control chromosomes in the GnomAD database, including 2,090 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 0.099 (2090 hom., cov: 32)
• Consequence: RAB11FIP2 NM_014904.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.33

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB11FIP2	NM_014904.3	c.353+2007G>A		intron_variant		ENST00000355624.8	NP_055719.1
RAB11FIP2	NM_001330167.2	c.353+2007G>A		intron_variant			NP_001317096.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAB11FIP2	ENST00000355624.8	c.353+2007G>A		intron_variant		1	NM_014904.3	ENSP00000347839	P1
	ENST00000451610.6	n.361-1472C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0986 AC: 14985 AN: 151992 Hom.: 2070 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0381

Gnomad ASJ AF: 0.00750

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0160

Gnomad FIN AF: 0.0232

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0143

Gnomad OTH AF: 0.0685

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0990 AC: 15055 AN: 152110 Hom.: 2090 Cov.: 32 AF XY: 0.0954 AC XY: 7091 AN XY: 74356

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.0380

Gnomad4 ASJ AF: 0.00750

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0158

Gnomad4 FIN AF: 0.0232

Gnomad4 NFE AF: 0.0144

Gnomad4 OTH AF: 0.0682

Alfa AF: 0.0721 Hom.: 204

Bravo AF: 0.110

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	15
DANN	Benign	0.53

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

LitVar

Other links and lift over

dbSNP: rs7095106; hg19: chr10-119803315;