10-118018124-C-T

Variant names:

• chr10-118018124-C-T
• rs2996224
• NM_014904.3:c.1266-3014G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014904.3(RAB11FIP2):​c.1266-3014G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0743 in 152,278 control chromosomes in the GnomAD database, including 759 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 0.074 (759 hom., cov: 33)
  • Exomes 𝑓: 0.063 (0 hom.)
• Consequence: RAB11FIP2 NM_014904.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.06
• Publications: 1 publications found

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]

ENSG00000231104 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014904.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB11FIP2	NM_014904.3	MANE Select	c.1266-3014G>A		intron	N/A	NP_055719.1	Q7L804-1
	RAB11FIP2	NM_001330167.2		c.1326-3014G>A		intron	N/A	NP_001317096.1	Q7L804-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB11FIP2	ENST00000355624.8	TSL:1 MANE Select	c.1266-3014G>A		intron	N/A	ENSP00000347839.3	Q7L804-1
	RAB11FIP2	ENST00000369199.5	TSL:1	c.1326-3014G>A		intron	N/A	ENSP00000358200.3	Q7L804-2
	RAB11FIP2	ENST00000895506.1		c.354-3014G>A		intron	N/A	ENSP00000565565.1

Frequencies

GnomAD3 genomes AF: 0.0743 AC: 11307 AN: 152144 Hom.: 758 Cov.: 33

Gnomad AFR AF: 0.0838

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0617

GnomAD4 exome AF: 0.0625 AC: 1 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.0625 AC XY: 1 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0833 AC: 1 AN: 12

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0743 AC: 11314 AN: 152262 Hom.: 759 Cov.: 33 AF XY: 0.0804 AC XY: 5983 AN XY: 74438

African (AFR) AF: 0.0836 AC: 3474 AN: 41550

American (AMR) AF: 0.102 AC: 1567 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0991 AC: 344 AN: 3472

East Asian (EAS) AF: 0.403 AC: 2083 AN: 5174

South Asian (SAS) AF: 0.105 AC: 505 AN: 4816

European-Finnish (FIN) AF: 0.0802 AC: 850 AN: 10602

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0342 AC: 2326 AN: 68036

Other (OTH) AF: 0.0611 AC: 129 AN: 2112

Alfa AF: 0.0544 Hom.: 47

Bravo AF: 0.0787

Asia WGS AF: 0.239 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	16
DANN	Benign	0.54
PhyloP100		2.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2996224; hg19: chr10-119777635;