17-31487044-G-A

Variant names:

• chr17-31487044-G-A
• rs11657523
• NM_032932.6:c.337-30607G>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.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
• Publications: 1 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=-0.87).
• 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 rank	MANE	Protein	UniProt
RAB11FIP4	NM_032932.6	c.337-30607G>A		intron_variant	Intron 3 of 14	ENST00000621161.5	NP_116321.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB11FIP4	ENST00000621161.5	c.337-30607G>A		intron_variant	Intron 3 of 14	1	NM_032932.6	ENSP00000482620.1
RAB11FIP4	ENST00000582009.5	c.205-30607G>A		intron_variant	Intron 3 of 4	3		ENSP00000463206.1

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

African (AFR) AF: 0.218 AC: 9052 AN: 41470

American (AMR) AF: 0.335 AC: 5121 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1647 AN: 3472

East Asian (EAS) AF: 0.437 AC: 2263 AN: 5184

South Asian (SAS) AF: 0.298 AC: 1433 AN: 4812

European-Finnish (FIN) AF: 0.409 AC: 4317 AN: 10546

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.454 AC: 30834 AN: 67948

Other (OTH) AF: 0.405 AC: 852 AN: 2106

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
PhyloP100		-0.26
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: rs11657523; hg19: chr17-29814062;