17-31495844-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.337-21807C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 152,066 control chromosomes in the GnomAD database, including 17,054 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 0.47 (17054 hom., cov: 32)
• Consequence: RAB11FIP4 NM_032932.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAB11FIP4	NM_032932.6	c.337-21807C>T		intron_variant		ENST00000621161.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAB11FIP4	ENST00000621161.5	c.337-21807C>T		intron_variant		1	NM_032932.6	P1

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71439 AN: 151948 Hom.: 17058 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.470 AC: 71461 AN: 152066 Hom.: 17054 Cov.: 32 AF XY: 0.461 AC XY: 34266 AN XY: 74334

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.490

Alfa AF: 0.460 Hom.: 3283

Bravo AF: 0.477

Asia WGS AF: 0.442 AC: 1535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	5.1
Dann	Benign	0.67

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: rs12937238; hg19: chr17-29822862;