rs10514203

Variant summary

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

The NM_006909.3(RASGRF2):​c.888-2461G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,290 control chromosomes in the GnomAD database, including 984 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 0.10 ( 984 hom., cov: 32)

Consequence

RASGRF2
NM_006909.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.600
Variant links:
Genes affected
RASGRF2 (HGNC:9876): (Ras protein specific guanine nucleotide releasing factor 2) RAS GTPases cycle between an inactive GDP-bound state and an active GTP-bound state. This gene encodes a calcium-regulated nucleotide exchange factor activating both RAS and RAS-related protein, RAC1, through the exchange of bound GDP for GTP, thereby, coordinating the signaling of distinct mitogen-activated protein kinase pathways. [provided by RefSeq, Oct 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RASGRF2NM_006909.3 linkuse as main transcriptc.888-2461G>A intron_variant ENST00000265080.9 NP_008840.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RASGRF2ENST00000265080.9 linkuse as main transcriptc.888-2461G>A intron_variant 1 NM_006909.3 ENSP00000265080 P1
RASGRF2ENST00000503795.1 linkuse as main transcriptc.888-2461G>A intron_variant, NMD_transcript_variant 1 ENSP00000421771
RASGRF2ENST00000638442.1 linkuse as main transcriptc.888-2461G>A intron_variant 5 ENSP00000491428
RASGRF2ENST00000502677.1 linkuse as main transcriptn.813-2461G>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.101
AC:
15410
AN:
152172
Hom.:
973
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.175
Gnomad AMI
AF:
0.108
Gnomad AMR
AF:
0.0754
Gnomad ASJ
AF:
0.0962
Gnomad EAS
AF:
0.00442
Gnomad SAS
AF:
0.0854
Gnomad FIN
AF:
0.0913
Gnomad MID
AF:
0.0601
Gnomad NFE
AF:
0.0731
Gnomad OTH
AF:
0.0865
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.102
AC:
15464
AN:
152290
Hom.:
984
Cov.:
32
AF XY:
0.101
AC XY:
7524
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.176
Gnomad4 AMR
AF:
0.0754
Gnomad4 ASJ
AF:
0.0962
Gnomad4 EAS
AF:
0.00443
Gnomad4 SAS
AF:
0.0863
Gnomad4 FIN
AF:
0.0913
Gnomad4 NFE
AF:
0.0731
Gnomad4 OTH
AF:
0.0847
Alfa
AF:
0.0753
Hom.:
697
Bravo
AF:
0.105
Asia WGS
AF:
0.0520
AC:
180
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
8.2
DANN
Benign
0.78

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: rs10514203; hg19: chr5-80373479; API