rs2271882

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.403
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE UniProt
RAB3ANM_002866.5 linkuse as main transcriptc.472+170T>C intron_variant ENST00000222256.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RAB3AENST00000222256.9 linkuse as main transcriptc.472+170T>C intron_variant 1 NM_002866.5 P1
RAB3AENST00000464076.3 linkuse as main transcriptc.187+170T>C intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.629
AC:
95516
AN:
151892
Hom.:
31175
Cov.:
31
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.552
Gnomad4 AMR
AF:
0.605
Gnomad4 ASJ
AF:
0.685
Gnomad4 EAS
AF:
0.157
Gnomad4 SAS
AF:
0.410
Gnomad4 FIN
AF:
0.788
Gnomad4 NFE
AF:
0.705
Gnomad4 OTH
AF:
0.644
Alfa
AF:
0.680
Hom.:
73459
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

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2271882; hg19: chr19-18309365; COSMIC: COSV55852883; COSMIC: COSV55852883; API