10-118018124-C-T

Position:

• chr10-118018124-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.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

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAB11FIP2	NM_014904.3	c.1266-3014G>A		intron_variant		ENST00000355624.8
RAB11FIP2	NM_001330167.2	c.1326-3014G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAB11FIP2	ENST00000355624.8	c.1266-3014G>A		intron_variant		1	NM_014904.3	P1
RAB11FIP2	ENST00000369199.5	c.1326-3014G>A		intron_variant		1
	ENST00000451610.6	n.163+475C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000595446.1	n.606C>T		non_coding_transcript_exon_variant	1/1

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

Gnomad4 ASJ exome AF: 0.00

Gnomad4 NFE exome AF: 0.0833

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.0836

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0991

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0802

Gnomad4 NFE AF: 0.0342

Gnomad4 OTH AF: 0.0611

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	16
DANN	Benign	0.54

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: rs2996224; hg19: chr10-119777635;