chr16-489140-C-A

Position:

• chr16-489140-C-A

Variant summary

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

The NM_014700.4(RAB11FIP3):​c.1265+140C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 1,046,724 control chromosomes in the GnomAD database, including 186,856 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 0.61 (29023 hom., cov: 33)
  • Exomes 𝑓: 0.59 (157833 hom.)
• Consequence: RAB11FIP3 NM_014700.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

Genes affected

RAB11FIP3 (HGNC:17224): (RAB11 family interacting protein 3) Proteins of the large Rab GTPase family (see RAB1A; MIM 179508) have regulatory roles in the formation, targeting, and fusion of intracellular transport vesicles. RAB11FIP3 is one of many proteins that interact with and regulate Rab GTPases (Hales et al., 2001 [PubMed 11495908]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB11FIP3	NM_014700.4	c.1265+140C>A		intron_variant		ENST00000262305.9	NP_055515.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAB11FIP3	ENST00000262305.9	c.1265+140C>A		intron_variant		1	NM_014700.4	ENSP00000262305

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93241 AN: 151900 Hom.: 29008 Cov.: 33

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.614

GnomAD4 exome AF: 0.590 AC: 527511 AN: 894706 Hom.: 157833 Cov.: 11 AF XY: 0.584 AC XY: 259244 AN XY: 443936

Gnomad4 AFR exome AF: 0.719

Gnomad4 AMR exome AF: 0.466

Gnomad4 ASJ exome AF: 0.592

Gnomad4 EAS exome AF: 0.490

Gnomad4 SAS exome AF: 0.412

Gnomad4 FIN exome AF: 0.616

Gnomad4 NFE exome AF: 0.604

Gnomad4 OTH exome AF: 0.592

GnomAD4 genome AF: 0.614 AC: 93302 AN: 152018 Hom.: 29023 Cov.: 33 AF XY: 0.607 AC XY: 45067 AN XY: 74306

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.612

Alfa AF: 0.597 Hom.: 12459

Bravo AF: 0.615

Asia WGS AF: 0.529 AC: 1843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.61
DANN	Benign	0.51

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: rs2038227; hg19: chr16-539140; COSMIC: COSV51932036; COSMIC: COSV51932036;