rs2271882

Variant names:

• chr19-18198555-A-G
• rs2271882
• NM_002866.5:c.472+170T>C

Your query was ambiguous. Multiple possible variants found:

• chr19-18198555-A-G
• chr19-18198555-A-T

Variant summary

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

The NM_002866.5(RAB3A):​c.472+170T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 152,010 control chromosomes in the GnomAD database, including 31,210 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 0.63 (31210 hom., cov: 31)
• Consequence: RAB3A NM_002866.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403
• Publications: 16 publications found

Genes affected

RAB3A (HGNC:9777): (RAB3A, member RAS oncogene family) Enables GTPase activity and myosin V binding activity. Involved in several processes, including acrosomal vesicle exocytosis; lysosome localization; and plasma membrane repair. Located in perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB3A	NM_002866.5	c.472+170T>C		intron_variant	Intron 4 of 4	ENST00000222256.9	NP_002857.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB3A	ENST00000222256.9	c.472+170T>C		intron_variant	Intron 4 of 4	1	NM_002866.5	ENSP00000222256.3
RAB3A	ENST00000464076.3	c.187+170T>C		intron_variant	Intron 3 of 3	2		ENSP00000474603.1

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95516 AN: 151892 Hom.: 31175 Cov.: 31

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.629 AC: 95617 AN: 152010 Hom.: 31210 Cov.: 31 AF XY: 0.626 AC XY: 46555 AN XY: 74312

African (AFR) AF: 0.552 AC: 22872 AN: 41438

American (AMR) AF: 0.605 AC: 9225 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2377 AN: 3470

East Asian (EAS) AF: 0.157 AC: 811 AN: 5166

South Asian (SAS) AF: 0.410 AC: 1979 AN: 4822

European-Finnish (FIN) AF: 0.788 AC: 8335 AN: 10584

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.705 AC: 47882 AN: 67964

Other (OTH) AF: 0.644 AC: 1357 AN: 2106

Alfa AF: 0.669 Hom.: 116873

Bravo AF: 0.614

Asia WGS AF: 0.318 AC: 1111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.41
PhyloP100		-0.40
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2271882; hg19: chr19-18309365; COSMIC: COSV55852883; COSMIC: COSV55852883;