rs2996224

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-118018124-C-G
• chr10-118018124-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014904.3(RAB11FIP2):​c.1266-3014G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• 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]

ENSG00000231104 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB11FIP2	NM_014904.3	c.1266-3014G>C		intron_variant	Intron 3 of 4	ENST00000355624.8	NP_055719.1
RAB11FIP2	NM_001330167.2	c.1326-3014G>C		intron_variant	Intron 4 of 5		NP_001317096.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB11FIP2	ENST00000355624.8	c.1266-3014G>C		intron_variant	Intron 3 of 4	1	NM_014904.3	ENSP00000347839.3
RAB11FIP2	ENST00000369199.5	c.1326-3014G>C		intron_variant	Intron 4 of 5	1		ENSP00000358200.3
ENSG00000231104	ENST00000595446.1	n.606C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000231104	ENST00000451610.6	n.163+475C>G		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	16
DANN	Benign	0.47

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;