rs11657523

Positions:

• chr17-31487044-G-A
• chr17-31487044-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.337-30607G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,012 control chromosomes in the GnomAD database, including 11,331 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 0.37 (11331 hom., cov: 32)
• Consequence: RAB11FIP4 NM_032932.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAB11FIP4	NM_032932.6	c.337-30607G>A		intron_variant		ENST00000621161.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAB11FIP4	ENST00000621161.5	c.337-30607G>A		intron_variant		1	NM_032932.6	P1
RAB11FIP4	ENST00000582009.5	c.205-30607G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56196 AN: 151894 Hom.: 11334 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.370 AC: 56186 AN: 152012 Hom.: 11331 Cov.: 32 AF XY: 0.364 AC XY: 27036 AN XY: 74282

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.405

Alfa AF: 0.396 Hom.: 1840

Bravo AF: 0.363

Asia WGS AF: 0.333 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
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: rs11657523; hg19: chr17-29814062;