rs17348624

Variant names:

• chr2-73084941-G-A
• rs17348624
• NM_001371272.1:c.1568+3109C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001371272.1(RAB11FIP5):​c.1568+3109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0584 in 152,298 control chromosomes in the GnomAD database, including 306 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 0.058 (306 hom., cov: 32)
• Consequence: RAB11FIP5 NM_001371272.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 5 publications found

Genes affected

RAB11FIP5 (HGNC:24845): (RAB11 family interacting protein 5) Enables gamma-tubulin binding activity. Involved in cellular response to acidic pH; negative regulation of adiponectin secretion; and regulation of protein localization to cell surface. Located in centriolar satellite and mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]

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 (EAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB11FIP5	NM_001371272.1	c.1568+3109C>T		intron_variant	Intron 3 of 5	ENST00000486777.7	NP_001358201.1
RAB11FIP5	NM_015470.3	c.1568+3109C>T		intron_variant	Intron 3 of 4		NP_056285.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB11FIP5	ENST00000486777.7	c.1568+3109C>T		intron_variant	Intron 3 of 5	5	NM_001371272.1	ENSP00000489752.1
RAB11FIP5	ENST00000258098.6	c.1568+3109C>T		intron_variant	Intron 3 of 4	1		ENSP00000258098.6
RAB11FIP5	ENST00000479196.1	n.279+3109C>T		intron_variant	Intron 1 of 1	3
RAB11FIP5	ENST00000493523.2	n.1477+3109C>T		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.0584 AC: 8891 AN: 152180 Hom.: 305 Cov.: 32

Gnomad AFR AF: 0.0536

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0336

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.0864

Gnomad FIN AF: 0.0309

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0607

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0584 AC: 8889 AN: 152298 Hom.: 306 Cov.: 32 AF XY: 0.0577 AC XY: 4296 AN XY: 74474

African (AFR) AF: 0.0536 AC: 2227 AN: 41570

American (AMR) AF: 0.0335 AC: 512 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0960 AC: 333 AN: 3470

East Asian (EAS) AF: 0.139 AC: 717 AN: 5176

South Asian (SAS) AF: 0.0861 AC: 415 AN: 4822

European-Finnish (FIN) AF: 0.0309 AC: 328 AN: 10620

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0606 AC: 4124 AN: 68020

Other (OTH) AF: 0.0682 AC: 144 AN: 2112

Alfa AF: 0.0584 Hom.: 60

Bravo AF: 0.0577

Asia WGS AF: 0.122 AC: 424 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	1.9
DANN	Benign	0.70
PhyloP100		-0.056
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: rs17348624; hg19: chr2-73312069;