2-73081095-TTCCTCCTCCTCCTCCTCCTCCTCC-TTCCTCCTCCTCCTCCTCCTCC

Variant names:

• chr2-73081095-TTCC-T
• rs72344675
• NM_001371272.1:c.2134_2136delGGA

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP3 BA1

The NM_001371272.1(RAB11FIP5):​c.2134_2136delGGA​(p.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 0.0164 in 1,227,106 control chromosomes in the GnomAD database, including 299 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.032 (133 hom., cov: 0)
  • Exomes 𝑓: 0.014 (166 hom.)
• Consequence: RAB11FIP5 NM_001371272.1 conservative_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• 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: Benign. The variant received -9 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_001371272.1
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB11FIP5	NM_001371272.1	c.2134_2136delGGA	p.Gly712del	conservative_inframe_deletion	Exon 4 of 6	ENST00000486777.7	NP_001358201.1
RAB11FIP5	NM_015470.3	c.1569-4916_1569-4914delGGA		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.2134_2136delGGA	p.Gly712del	conservative_inframe_deletion	Exon 4 of 6	5	NM_001371272.1	ENSP00000489752.1

Frequencies

GnomAD3 genomes AF: 0.0319 AC: 4779 AN: 149614 Hom.: 132 Cov.: 0

Gnomad AFR AF: 0.0779

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0222

Gnomad ASJ AF: 0.0119

Gnomad EAS AF: 0.00180

Gnomad SAS AF: 0.0154

Gnomad FIN AF: 0.0145

Gnomad MID AF: 0.0160

Gnomad NFE AF: 0.0142

Gnomad OTH AF: 0.0210

GnomAD4 exome AF: 0.0143 AC: 15357 AN: 1077390 Hom.: 166 AF XY: 0.0141 AC XY: 7164 AN XY: 509226

African (AFR) AF: 0.0829 AC: 1886 AN: 22762

American (AMR) AF: 0.0181 AC: 152 AN: 8376

Ashkenazi Jewish (ASJ) AF: 0.00991 AC: 142 AN: 14326

East Asian (EAS) AF: 0.00151 AC: 40 AN: 26462

South Asian (SAS) AF: 0.0121 AC: 236 AN: 19468

European-Finnish (FIN) AF: 0.0105 AC: 225 AN: 21402

Middle Eastern (MID) AF: 0.0193 AC: 57 AN: 2950

European-Non Finnish (NFE) AF: 0.0129 AC: 11859 AN: 918066

Other (OTH) AF: 0.0174 AC: 760 AN: 43578

GnomAD4 genome AF: 0.0320 AC: 4789 AN: 149716 Hom.: 133 Cov.: 0 AF XY: 0.0317 AC XY: 2315 AN XY: 73076

African (AFR) AF: 0.0780 AC: 3182 AN: 40804

American (AMR) AF: 0.0222 AC: 335 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.0119 AC: 41 AN: 3442

East Asian (EAS) AF: 0.00181 AC: 9 AN: 4976

South Asian (SAS) AF: 0.0153 AC: 72 AN: 4716

European-Finnish (FIN) AF: 0.0145 AC: 150 AN: 10342

Middle Eastern (MID) AF: 0.0172 AC: 5 AN: 290

European-Non Finnish (NFE) AF: 0.0142 AC: 952 AN: 67076

Other (OTH) AF: 0.0208 AC: 43 AN: 2066

Alfa AF: 0.00361 Hom.: 103

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.22
Mutation Taster		=100/0	polymorphism

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: rs72344675; hg19: chr2-73308223;