17-31495844-C-T

Variant names:

• chr17-31495844-C-T
• rs12937238
• NM_032932.6:c.337-21807C>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.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
• Publications: 4 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 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.337-21807C>T		intron	N/A	NP_116321.2
	RAB11FIP4	NM_001303542.3		c.30+7572C>T		intron	N/A	NP_001290471.2	Q86YS3-2
	RAB11FIP4	NM_001346748.2		c.-88+7412C>T		intron	N/A	NP_001333677.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB11FIP4	ENST00000621161.5	TSL:1 MANE Select	c.337-21807C>T		intron	N/A	ENSP00000482620.1	Q86YS3-1
	RAB11FIP4	ENST00000964368.1		c.337-21807C>T		intron	N/A	ENSP00000634427.1
	RAB11FIP4	ENST00000394744.6	TSL:2	c.30+7572C>T		intron	N/A	ENSP00000378227.2	Q86YS3-2

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

African (AFR) AF: 0.527 AC: 21859 AN: 41486

American (AMR) AF: 0.394 AC: 6026 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1787 AN: 3468

East Asian (EAS) AF: 0.560 AC: 2900 AN: 5174

South Asian (SAS) AF: 0.335 AC: 1617 AN: 4820

European-Finnish (FIN) AF: 0.408 AC: 4309 AN: 10556

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31242 AN: 67954

Other (OTH) AF: 0.490 AC: 1035 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.1
DANN	Benign	0.67
PhyloP100		-0.17
Mutation Taster		=99/1	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: rs12937238; hg19: chr17-29822862;