rs178858

Positions:

• chr17-31446733-G-A
• chr17-31446733-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.336+12611G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,976 control chromosomes in the GnomAD database, including 9,610 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 0.35 (9610 hom., cov: 31)
• Consequence: RAB11FIP4 NM_032932.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

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]

RAB11FIP4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB11FIP4	NM_032932.6	c.336+12611G>A		intron_variant		ENST00000621161.5	NP_116321.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAB11FIP4	ENST00000621161.5	c.336+12611G>A		intron_variant		1	NM_032932.6	ENSP00000482620.1
RAB11FIP4	ENST00000582009.5	c.204+12611G>A		intron_variant		3		ENSP00000463206.1
RAB11FIP4	ENST00000579908.1	n.178-1684G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53626 AN: 151858 Hom.: 9602 Cov.: 31

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.353 AC: 53656 AN: 151976 Hom.: 9610 Cov.: 31 AF XY: 0.354 AC XY: 26340 AN XY: 74304

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.320

Alfa AF: 0.352 Hom.: 19428

Bravo AF: 0.349

Asia WGS AF: 0.346 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.53
DANN	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs178858; hg19: chr17-29773751;