17-31473638-C-T

Variant names:

• chr17-31473638-C-T
• rs178900
• NM_032932.6:c.336+39516C>T

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+39516C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 152,116 control chromosomes in the GnomAD database, including 45,447 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 0.77 (45447 hom., cov: 32)
• Consequence: RAB11FIP4 NM_032932.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 9 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 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.336+39516C>T		intron	N/A	NP_116321.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB11FIP4	ENST00000621161.5	TSL:1 MANE Select	c.336+39516C>T		intron	N/A	ENSP00000482620.1	Q86YS3-1
	RAB11FIP4	ENST00000964368.1		c.336+39516C>T		intron	N/A	ENSP00000634427.1
	RAB11FIP4	ENST00000582009.5	TSL:3	c.204+39516C>T		intron	N/A	ENSP00000463206.1	J3QKR9

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117314 AN: 151998 Hom.: 45424 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.772 AC: 117387 AN: 152116 Hom.: 45447 Cov.: 32 AF XY: 0.770 AC XY: 57230 AN XY: 74350

African (AFR) AF: 0.818 AC: 33971 AN: 41508

American (AMR) AF: 0.712 AC: 10883 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2716 AN: 3470

East Asian (EAS) AF: 0.921 AC: 4754 AN: 5162

South Asian (SAS) AF: 0.799 AC: 3854 AN: 4824

European-Finnish (FIN) AF: 0.729 AC: 7696 AN: 10560

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 51001 AN: 67994

Other (OTH) AF: 0.750 AC: 1582 AN: 2110

Alfa AF: 0.758 Hom.: 122772

Bravo AF: 0.771

Asia WGS AF: 0.837 AC: 2912 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.36
PhyloP100		-1.7
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: rs178900; hg19: chr17-29800656;