17-31530789-G-C

Position:

• chr17-31530789-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB11FIP4	NM_032932.6	c.1797+320G>C		intron_variant		ENST00000621161.5	NP_116321.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAB11FIP4	ENST00000621161.5	c.1797+320G>C		intron_variant		1	NM_032932.6	ENSP00000482620	P1
RAB11FIP4	ENST00000394744.6	c.1491+320G>C		intron_variant		2		ENSP00000378227

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

Gnomad4 AFR AF: 0.864

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.794

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.713

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.43

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: rs2074153; hg19: chr17-29857807;