2-73081095-TTCCTCCTCCTCCTCCTCCTCCTCC-TTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC

Variant names:

• chr2-73081095-T-TTCCTCCTCC
• rs72344675
• NM_001371272.1:c.2128_2136dupGGAGGAGGA

Variant summary

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

The NM_001371272.1(RAB11FIP5):​c.2128_2136dupGGAGGAGGA​(p.Gly710_Gly712dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00034 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000040 (0 hom.)
• Consequence: RAB11FIP5 NM_001371272.1 conservative_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• 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_2136dupGGAGGAGGA	p.Gly710_Gly712dup	conservative_inframe_insertion	Exon 4 of 6	ENST00000486777.7	NP_001358201.1
RAB11FIP5	NM_015470.3	c.1569-4922_1569-4914dupGGAGGAGGA		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_2136dupGGAGGAGGA	p.Gly710_Gly712dup	conservative_inframe_insertion	Exon 4 of 6	5	NM_001371272.1	ENSP00000489752.1

Frequencies

GnomAD3 genomes AF: 0.000341 AC: 51 AN: 149636 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00115

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000423

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000149

Gnomad OTH AF: 0.000489

GnomAD4 exome AF: 0.0000398 AC: 43 AN: 1080168 Hom.: 0 Cov.: 4 AF XY: 0.0000372 AC XY: 19 AN XY: 510580

African (AFR) AF: 0.00105 AC: 24 AN: 22776

American (AMR) AF: 0.000119 AC: 1 AN: 8438

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

East Asian (EAS) AF: 0.0000378 AC: 1 AN: 26490

South Asian (SAS) AF: 0.00 AC: 0 AN: 19508

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21534

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2954

European-Non Finnish (NFE) AF: 0.00000652 AC: 6 AN: 920352

Other (OTH) AF: 0.000252 AC: 11 AN: 43730

GnomAD4 genome AF: 0.000341 AC: 51 AN: 149738 Hom.: 0 Cov.: 0 AF XY: 0.000328 AC XY: 24 AN XY: 73094

African (AFR) AF: 0.00115 AC: 47 AN: 40814

American (AMR) AF: 0.00 AC: 0 AN: 15104

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 4976

South Asian (SAS) AF: 0.000424 AC: 2 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: 0.0000149 AC: 1 AN: 67086

Other (OTH) AF: 0.000484 AC: 1 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		0.042
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;