rs17348624

chr2-73084941-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
RAB11FIP5	NM_001371272.1	c.1568+3109C>T		intron_variant		ENST00000486777.7
RAB11FIP5	NM_015470.3	c.1568+3109C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAB11FIP5	ENST00000486777.7	c.1568+3109C>T		intron_variant		5	NM_001371272.1
RAB11FIP5	ENST00000258098.6	c.1568+3109C>T		intron_variant		1		P1
RAB11FIP5	ENST00000479196.1	n.279+3109C>T		intron_variant, non_coding_transcript_variant		3
RAB11FIP5	ENST00000493523.2	n.1477+3109C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0536

Gnomad4 AMR AF: 0.0335

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.0861

Gnomad4 FIN AF: 0.0309

Gnomad4 NFE AF: 0.0606

Gnomad4 OTH AF: 0.0682

Alfa AF: 0.0578 Hom.: 59

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

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: rs17348624; hg19: chr2-73312069;