chr17-31508205-G-A

Variant names:

• chr17-31508205-G-A
• rs2343245
• NM_032932.6:c.337-9446G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032932.6(RAB11FIP4):​c.337-9446G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 151,958 control chromosomes in the GnomAD database, including 30,674 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 0.63 (30674 hom., cov: 31)
• Consequence: RAB11FIP4 NM_032932.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.837
• Publications: 3 publications found

Genes affected

RAB11FIP4 (HGNC:30267): (RAB11 family interacting protein 4) The protein encoded by this gene interacts with RAB11 and is thought to be involved in bringing recycling endosome membranes to the cleavage furrow in late cytokinesis. Hypoxic conditions can lead to an upregulation of the encoded protein and enhance the metastatic potential of hepatocellular carcinoma. [provided by RefSeq, Oct 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032932.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB11FIP4	NM_032932.6	MANE Select	c.337-9446G>A		intron	N/A	NP_116321.2
	RAB11FIP4	NM_001303542.3		c.31-9446G>A		intron	N/A	NP_001290471.2	Q86YS3-2
	RAB11FIP4	NM_001346748.2		c.-87-9446G>A		intron	N/A	NP_001333677.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB11FIP4	ENST00000621161.5	TSL:1 MANE Select	c.337-9446G>A		intron	N/A	ENSP00000482620.1	Q86YS3-1
	RAB11FIP4	ENST00000964368.1		c.337-9446G>A		intron	N/A	ENSP00000634427.1
	RAB11FIP4	ENST00000394744.6	TSL:2	c.31-9446G>A		intron	N/A	ENSP00000378227.2	Q86YS3-2

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96367 AN: 151840 Hom.: 30681 Cov.: 31

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.634 AC: 96393 AN: 151958 Hom.: 30674 Cov.: 31 AF XY: 0.630 AC XY: 46789 AN XY: 74284

African (AFR) AF: 0.621 AC: 25718 AN: 41396

American (AMR) AF: 0.563 AC: 8605 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2458 AN: 3472

East Asian (EAS) AF: 0.687 AC: 3556 AN: 5176

South Asian (SAS) AF: 0.613 AC: 2950 AN: 4814

European-Finnish (FIN) AF: 0.679 AC: 7190 AN: 10584

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43693 AN: 67926

Other (OTH) AF: 0.648 AC: 1367 AN: 2108

Alfa AF: 0.634 Hom.: 3936

Bravo AF: 0.629

Asia WGS AF: 0.630 AC: 2186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.8
DANN	Benign	0.43
PhyloP100		0.84
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: rs2343245; hg19: chr17-29835223;