17-31530789-G-C

Variant names:

• chr17-31530789-G-C
• rs2074153
• NM_032932.6:c.1797+320G>C

Variant summary

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

The NM_032932.6(RAB11FIP4):​c.1797+320G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,112 control chromosomes in the GnomAD database, including 39,353 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 0.71 (39353 hom., cov: 32)
• Consequence: RAB11FIP4 NM_032932.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.829
• Publications: 4 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB11FIP4	NM_032932.6	MANE Select	c.1797+320G>C		intron	N/A	NP_116321.2
	RAB11FIP4	NM_001303542.3		c.1491+320G>C		intron	N/A	NP_001290471.2
	RAB11FIP4	NM_001346748.2		c.1374+320G>C		intron	N/A	NP_001333677.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB11FIP4	ENST00000621161.5	TSL:1 MANE Select	c.1797+320G>C		intron	N/A	ENSP00000482620.1
	RAB11FIP4	ENST00000394744.6	TSL:2	c.1491+320G>C		intron	N/A	ENSP00000378227.2
	RAB11FIP4	ENST00000578148.1	TSL:3	n.-183G>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108339 AN: 151994 Hom.: 39293 Cov.: 32

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.713 AC: 108454 AN: 152112 Hom.: 39353 Cov.: 32 AF XY: 0.708 AC XY: 52658 AN XY: 74350

African (AFR) AF: 0.864 AC: 35864 AN: 41522

American (AMR) AF: 0.596 AC: 9097 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2542 AN: 3468

East Asian (EAS) AF: 0.794 AC: 4105 AN: 5170

South Asian (SAS) AF: 0.583 AC: 2812 AN: 4822

European-Finnish (FIN) AF: 0.673 AC: 7132 AN: 10592

Middle Eastern (MID) AF: 0.712 AC: 208 AN: 292

European-Non Finnish (NFE) AF: 0.656 AC: 44556 AN: 67960

Other (OTH) AF: 0.713 AC: 1505 AN: 2112

Alfa AF: 0.543 Hom.: 1180

Bravo AF: 0.715

Asia WGS AF: 0.705 AC: 2450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.43
PhyloP100		-0.83
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: rs2074153; hg19: chr17-29857807;