2-73081095-TTCCTCCTCCTCCTCCTCCTCCTCC-TTCCTCCTCCTCC

Variant names:

• chr2-73081095-TTCCTCCTCCTCC-T
• rs72344675
• NM_001371272.1:c.2125_2136delGGAGGAGGAGGA

Variant summary

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

The NM_001371272.1(RAB11FIP5):​c.2125_2136delGGAGGAGGAGGA​(p.Gly709_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 0.000143 in 1,229,906 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00014 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00014 (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.2125_2136delGGAGGAGGAGGA	p.Gly709_Gly712del	conservative_inframe_deletion	Exon 4 of 6	ENST00000486777.7	NP_001358201.1
RAB11FIP5	NM_015470.3	c.1569-4925_1569-4914delGGAGGAGGAGGA		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.2125_2136delGGAGGAGGAGGA	p.Gly709_Gly712del	conservative_inframe_deletion	Exon 4 of 6	5	NM_001371272.1	ENSP00000489752.1

Frequencies

GnomAD3 genomes AF: 0.000140 AC: 21 AN: 149636 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000246

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000663

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00120

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000194

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000143 AC: 155 AN: 1080168 Hom.: 0 AF XY: 0.000133 AC XY: 68 AN XY: 510580

African (AFR) AF: 0.00 AC: 0 AN: 22776

American (AMR) AF: 0.00 AC: 0 AN: 8438

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14386

East Asian (EAS) AF: 0.000717 AC: 19 AN: 26490

South Asian (SAS) AF: 0.0000513 AC: 1 AN: 19508

European-Finnish (FIN) AF: 0.0000464 AC: 1 AN: 21534

Middle Eastern (MID) AF: 0.000677 AC: 2 AN: 2954

European-Non Finnish (NFE) AF: 0.000139 AC: 128 AN: 920352

Other (OTH) AF: 0.0000915 AC: 4 AN: 43730

GnomAD4 genome AF: 0.000140 AC: 21 AN: 149738 Hom.: 0 Cov.: 0 AF XY: 0.000123 AC XY: 9 AN XY: 73094

African (AFR) AF: 0.0000245 AC: 1 AN: 40814

American (AMR) AF: 0.0000662 AC: 1 AN: 15104

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

East Asian (EAS) AF: 0.00121 AC: 6 AN: 4976

South Asian (SAS) AF: 0.00 AC: 0 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: 0.000194 AC: 13 AN: 67086

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

Alfa AF: 0.0000802 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;