2-237590801-C-T

Variant names:

• chr2-237590801-C-T
• rs2292873
• ENST00000392001.6:n.-338G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000392001.6(RAB17):​n.-338G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 156,594 control chromosomes in the GnomAD database, including 1,104 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 0.11 (1098 hom., cov: 32)
  • Exomes 𝑓: 0.035 (6 hom.)
• Consequence: RAB17 ENST00000392001.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701
• Publications: 11 publications found

Genes affected

RAB17 (HGNC:16523): (RAB17, member RAS oncogene family) The Rab subfamily of small GTPases plays an important role in the regulation of membrane trafficking. RAB17 is an epithelial cell-specific GTPase (Lutcke et al., 1993 [PubMed 8486736]).[supplied by OMIM, Oct 2009]

RAB17-DT (HGNC:56028): (RAB17 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB17	NM_022449.4	c.-338G>A		upstream_gene_variant		ENST00000264601.8	NP_071894.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB17	ENST00000264601.8	c.-338G>A		upstream_gene_variant		1	NM_022449.4	ENSP00000264601.3

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17161 AN: 152008 Hom.: 1100 Cov.: 32

Gnomad AFR AF: 0.0858

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.0680

Gnomad ASJ AF: 0.0629

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.0887

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.106

GnomAD4 exome AF: 0.0349 AC: 156 AN: 4468 Hom.: 6 Cov.: 0 AF XY: 0.0355 AC XY: 84 AN XY: 2368

African (AFR) AF: 0.00 AC: 0 AN: 20

American (AMR) AF: 0.00746 AC: 1 AN: 134

Ashkenazi Jewish (ASJ) AF: 0.00877 AC: 1 AN: 114

East Asian (EAS) AF: 0.00 AC: 0 AN: 32

South Asian (SAS) AF: 0.0318 AC: 18 AN: 566

European-Finnish (FIN) AF: 0.0250 AC: 9 AN: 360

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 16

European-Non Finnish (NFE) AF: 0.0402 AC: 118 AN: 2938

Other (OTH) AF: 0.0313 AC: 9 AN: 288

GnomAD4 genome AF: 0.113 AC: 17159 AN: 152126 Hom.: 1098 Cov.: 32 AF XY: 0.111 AC XY: 8222 AN XY: 74378

African (AFR) AF: 0.0856 AC: 3553 AN: 41488

American (AMR) AF: 0.0679 AC: 1038 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0629 AC: 218 AN: 3468

East Asian (EAS) AF: 0.122 AC: 629 AN: 5164

South Asian (SAS) AF: 0.0885 AC: 426 AN: 4812

European-Finnish (FIN) AF: 0.128 AC: 1357 AN: 10588

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9509 AN: 67992

Other (OTH) AF: 0.105 AC: 222 AN: 2114

Alfa AF: 0.127 Hom.: 3716

Bravo AF: 0.106

Asia WGS AF: 0.0750 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.2
DANN	Benign	0.71
PhyloP100		-0.70
PromoterAI		-0.077	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=300/0	polymorphism (auto)

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: rs2292873; hg19: chr2-238499444;