rs9437

Variant names:

• chr8-60622858-G-A
• rs9437
• NM_002865.3:c.*2089G>A

Variant summary

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

The NM_002865.3(RAB2A):​c.*2089G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,020 control chromosomes in the GnomAD database, including 4,483 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 0.24 (4483 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: RAB2A NM_002865.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 5 publications found

Genes affected

RAB2A (HGNC:9763): (RAB2A, member RAS oncogene family) The protein encoded by this gene belongs to the Rab family, members of which are small molecular weight guanosine triphosphatases (GTPases) that contain highly conserved domains involved in GTP binding and hydrolysis. The Rabs are membrane-bound proteins, involved in vesicular fusion and trafficking. This protein is a resident of pre-Golgi intermediates, and is required for protein transport from the endoplasmic reticulum (ER) to the Golgi complex. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB2A	NM_002865.3	c.*2089G>A		3_prime_UTR_variant	Exon 8 of 8	ENST00000262646.12	NP_002856.1
RAB2A	NM_001242644.1	c.*2089G>A		3_prime_UTR_variant	Exon 7 of 7		NP_001229573.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB2A	ENST00000262646.12	c.*2089G>A		3_prime_UTR_variant	Exon 8 of 8	1	NM_002865.3	ENSP00000262646.7

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36697 AN: 151902 Hom.: 4474 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.0925

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.264

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.242 AC: 36738 AN: 152020 Hom.: 4483 Cov.: 33 AF XY: 0.240 AC XY: 17812 AN XY: 74312

African (AFR) AF: 0.244 AC: 10109 AN: 41458

American (AMR) AF: 0.231 AC: 3524 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1202 AN: 3466

East Asian (EAS) AF: 0.289 AC: 1496 AN: 5178

South Asian (SAS) AF: 0.316 AC: 1521 AN: 4818

European-Finnish (FIN) AF: 0.161 AC: 1707 AN: 10572

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16414 AN: 67950

Other (OTH) AF: 0.267 AC: 563 AN: 2110

Alfa AF: 0.237 Hom.: 768

Bravo AF: 0.246

Asia WGS AF: 0.310 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.015
DANN	Benign	0.28
PhyloP100		-1.8
Mutation Taster		=100/0	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: rs9437; hg19: chr8-61535417;