rs7812866

Variant names:

• chr8-37892771-A-C
• rs7812866
• NM_001002814.3:c.371+6300T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-37892771-A-C
• chr8-37892771-A-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RAB11FIP1	NM_001002814.3	c.371+6300T>G		intron_variant	Intron 1 of 5	ENST00000330843.9	NP_001002814.2
RAB11FIP1	NM_025151.5	c.371+6300T>G		intron_variant	Intron 1 of 4		NP_079427.4
RAB11FIP1	XM_017013869.2	c.371+6300T>G		intron_variant	Intron 1 of 3		XP_016869358.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB11FIP1	ENST00000330843.9	c.371+6300T>G		intron_variant	Intron 1 of 5	1	NM_001002814.3	ENSP00000331342.4
RAB11FIP1	ENST00000287263.8	c.371+6300T>G		intron_variant	Intron 1 of 4	1		ENSP00000287263.4
RAB11FIP1	ENST00000522727.5	c.-74+6533T>G		intron_variant	Intron 1 of 4	1		ENSP00000430009.1

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

African (AFR) AF: 0.525 AC: 21724 AN: 41394

American (AMR) AF: 0.440 AC: 6717 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1616 AN: 3472

East Asian (EAS) AF: 0.263 AC: 1357 AN: 5150

South Asian (SAS) AF: 0.389 AC: 1876 AN: 4826

European-Finnish (FIN) AF: 0.470 AC: 4943 AN: 10526

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.479 AC: 32551 AN: 67948

Other (OTH) AF: 0.446 AC: 936 AN: 2100

Alfa AF: 0.474 Hom.: 73374

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
PhyloP100		-0.99
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: rs7812866; hg19: chr8-37750289;