17-31473638-C-T

Position:

• chr17-31473638-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB11FIP4	NM_032932.6	c.336+39516C>T		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+39516C>T		intron_variant		1	NM_032932.6	ENSP00000482620	P1
RAB11FIP4	ENST00000582009.5	c.204+39516C>T		intron_variant		3		ENSP00000463206

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

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.750

Alfa AF: 0.755 Hom.: 82991

Bravo AF: 0.771

Asia WGS AF: 0.837 AC: 2912 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.36

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: rs178900; hg19: chr17-29800656;