rs13391694

Variant summary

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

The NM_001139488.2(RASGRP3):​c.-261+15909G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,956 control chromosomes in the GnomAD database, including 13,901 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 0.42 ( 13901 hom., cov: 32)

Consequence

RASGRP3
NM_001139488.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07
Variant links:
Genes affected
RASGRP3 (HGNC:14545): (RAS guanyl releasing protein 3) The protein encoded by this gene is a guanine nucleotide exchange factor that activates the oncogenes HRAS and RAP1A. Defects in this gene have been associated with systemic lupus erythematosus and several cancers. [provided by RefSeq, Mar 2017]

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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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RASGRP3NM_001139488.2 linkuse as main transcriptc.-261+15909G>A intron_variant ENST00000403687.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RASGRP3ENST00000403687.8 linkuse as main transcriptc.-261+15909G>A intron_variant 1 NM_001139488.2 P5Q8IV61-1

Frequencies

GnomAD3 genomes
AF:
0.415
AC:
62985
AN:
151838
Hom.:
13850
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.561
Gnomad AMI
AF:
0.395
Gnomad AMR
AF:
0.433
Gnomad ASJ
AF:
0.314
Gnomad EAS
AF:
0.365
Gnomad SAS
AF:
0.388
Gnomad FIN
AF:
0.388
Gnomad MID
AF:
0.345
Gnomad NFE
AF:
0.339
Gnomad OTH
AF:
0.376
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.415
AC:
63107
AN:
151956
Hom.:
13901
Cov.:
32
AF XY:
0.417
AC XY:
30991
AN XY:
74276
show subpopulations
Gnomad4 AFR
AF:
0.561
Gnomad4 AMR
AF:
0.434
Gnomad4 ASJ
AF:
0.314
Gnomad4 EAS
AF:
0.366
Gnomad4 SAS
AF:
0.388
Gnomad4 FIN
AF:
0.388
Gnomad4 NFE
AF:
0.339
Gnomad4 OTH
AF:
0.381
Alfa
AF:
0.353
Hom.:
8995
Bravo
AF:
0.425
Asia WGS
AF:
0.403
AC:
1400
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.070
DANN
Benign
0.22

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

Publications

LitVar

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

Other links and lift over

dbSNP: rs13391694; hg19: chr2-33717683; API