8-60610351-C-T

Variant names:

• chr8-60610351-C-T
• rs595255
• NM_002865.3:c.475-8229C>T

Variant summary

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

The NM_002865.3(RAB2A):​c.475-8229C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 152,094 control chromosomes in the GnomAD database, including 24,522 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 0.53 (24522 hom., cov: 32)
• Consequence: RAB2A NM_002865.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB2A	NM_002865.3	c.475-8229C>T		intron_variant	Intron 6 of 7	ENST00000262646.12	NP_002856.1
RAB2A	NM_001242644.1	c.403-8229C>T		intron_variant	Intron 5 of 6		NP_001229573.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB2A	ENST00000262646.12	c.475-8229C>T		intron_variant	Intron 6 of 7	1	NM_002865.3	ENSP00000262646.7

Frequencies

GnomAD3 genomes AF: 0.533 AC: 81025 AN: 151976 Hom.: 24473 Cov.: 32

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.528

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.533 AC: 81138 AN: 152094 Hom.: 24522 Cov.: 32 AF XY: 0.536 AC XY: 39844 AN XY: 74340

African (AFR) AF: 0.832 AC: 34545 AN: 41506

American (AMR) AF: 0.443 AC: 6771 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1774 AN: 3470

East Asian (EAS) AF: 0.569 AC: 2940 AN: 5170

South Asian (SAS) AF: 0.621 AC: 2991 AN: 4820

European-Finnish (FIN) AF: 0.451 AC: 4771 AN: 10572

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25819 AN: 67964

Other (OTH) AF: 0.530 AC: 1117 AN: 2106

Alfa AF: 0.395 Hom.: 2355

Bravo AF: 0.542

Asia WGS AF: 0.649 AC: 2258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.50
PhyloP100		0.41
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: rs595255; hg19: chr8-61522910;