2-73081095-TTCCTCCTCCTCCTCCTCCTCCTCC-TTCCTCCTCCTCCTCC

Variant names:

• chr2-73081095-TTCCTCCTCC-T
• rs72344675
• NM_001371272.1:c.2128_2136delGGAGGAGGA

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3

The NM_001371272.1(RAB11FIP5):​c.2128_2136delGGAGGAGGA​(p.Gly710_Gly712del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00017 in 1,227,060 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00045 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00013 (0 hom.)
• Consequence: RAB11FIP5 NM_001371272.1 conservative_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 1 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: Likely_benign. The variant received -1 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_001371272.1

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB11FIP5	NM_001371272.1	c.2128_2136delGGAGGAGGA	p.Gly710_Gly712del	conservative_inframe_deletion	Exon 4 of 6	ENST00000486777.7	NP_001358201.1
RAB11FIP5	NM_015470.3	c.1569-4922_1569-4914delGGAGGAGGA		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.2128_2136delGGAGGAGGA	p.Gly710_Gly712del	conservative_inframe_deletion	Exon 4 of 6	5	NM_001371272.1	ENSP00000489752.1

Frequencies

GnomAD3 genomes AF: 0.000454 AC: 68 AN: 149634 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00133

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000331

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000802

Gnomad SAS AF: 0.000212

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000596

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000131 AC: 141 AN: 1077324 Hom.: 0 AF XY: 0.000128 AC XY: 65 AN XY: 509238

African (AFR) AF: 0.00129 AC: 29 AN: 22490

American (AMR) AF: 0.00 AC: 0 AN: 8408

Ashkenazi Jewish (ASJ) AF: 0.0000697 AC: 1 AN: 14342

East Asian (EAS) AF: 0.000191 AC: 5 AN: 26212

South Asian (SAS) AF: 0.000154 AC: 3 AN: 19418

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21490

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2946

European-Non Finnish (NFE) AF: 0.000105 AC: 96 AN: 918454

Other (OTH) AF: 0.000161 AC: 7 AN: 43564

GnomAD4 genome AF: 0.000454 AC: 68 AN: 149736 Hom.: 0 Cov.: 0 AF XY: 0.000465 AC XY: 34 AN XY: 73092

African (AFR) AF: 0.00132 AC: 54 AN: 40814

American (AMR) AF: 0.000331 AC: 5 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3442

East Asian (EAS) AF: 0.000804 AC: 4 AN: 4976

South Asian (SAS) AF: 0.000212 AC: 1 AN: 4716

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10344

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.0000596 AC: 4 AN: 67084

Other (OTH) AF: 0.00 AC: 0 AN: 2066

Alfa AF: 0.00 Hom.: 103

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs72344675; hg19: chr2-73308223;