chr17-31446733-G-A

Variant names:

• chr17-31446733-G-A
• rs178858
• NM_032932.6:c.336+12611G>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.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
• Publications: 10 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.402 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.336+12611G>A		intron	N/A	NP_116321.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB11FIP4	ENST00000621161.5	TSL:1 MANE Select	c.336+12611G>A		intron	N/A	ENSP00000482620.1
	RAB11FIP4	ENST00000582009.5	TSL:3	c.204+12611G>A		intron	N/A	ENSP00000463206.1
	RAB11FIP4	ENST00000579908.1	TSL:3	n.178-1684G>A		intron	N/A

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

African (AFR) AF: 0.340 AC: 14077 AN: 41440

American (AMR) AF: 0.362 AC: 5529 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1021 AN: 3466

East Asian (EAS) AF: 0.284 AC: 1465 AN: 5160

South Asian (SAS) AF: 0.417 AC: 2011 AN: 4818

European-Finnish (FIN) AF: 0.389 AC: 4101 AN: 10554

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24324 AN: 67946

Other (OTH) AF: 0.320 AC: 675 AN: 2112

Alfa AF: 0.354 Hom.: 31512

Bravo AF: 0.349

Asia WGS AF: 0.346 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.53
DANN	Benign	0.79
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs178858; hg19: chr17-29773751;