8-37892771-A-C

Position:

• chr8-37892771-A-C

Variant summary

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

The NM_001002814.3(RAB11FIP1):​c.371+6300T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,878 control chromosomes in the GnomAD database, including 17,366 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 0.48 (17366 hom., cov: 31)
• Consequence: RAB11FIP1 NM_001002814.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986

Genes affected

RAB11FIP1 (HGNC:30265): (RAB11 family interacting protein 1) This gene encodes one of the Rab11-family interacting proteins (Rab11-FIPs), which play a role in the Rab-11 mediated recycling of vesicles. The encoded protein may be involved in endocytic sorting, trafficking of proteins including integrin subunits and epidermal growth factor receptor (EGFR), and transport between the recycling endosome and the trans-Golgi network. Alternative splicing results in multiple transcript variants. A pseudogene is described on the X chromosome. [provided by RefSeq, Dec 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB11FIP1	NM_001002814.3	c.371+6300T>G		intron_variant		ENST00000330843.9	NP_001002814.2
RAB11FIP1	NM_025151.5	c.371+6300T>G		intron_variant			NP_079427.4
RAB11FIP1	XM_017013869.2	c.371+6300T>G		intron_variant			XP_016869358.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAB11FIP1	ENST00000330843.9	c.371+6300T>G		intron_variant		1	NM_001002814.3	ENSP00000331342	A2
RAB11FIP1	ENST00000287263.8	c.371+6300T>G		intron_variant		1		ENSP00000287263	P2
RAB11FIP1	ENST00000522727.5	c.-74+6533T>G		intron_variant		1		ENSP00000430009

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72138 AN: 151762 Hom.: 17333 Cov.: 31

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.475 AC: 72214 AN: 151878 Hom.: 17366 Cov.: 31 AF XY: 0.471 AC XY: 34969 AN XY: 74204

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.446

Alfa AF: 0.472 Hom.: 34251

Bravo AF: 0.474

Asia WGS AF: 0.354 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.84

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: rs7812866; hg19: chr8-37750289;