19-38411347-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_170604.3(RASGRP4):​c.1715G>A​(p.Arg572Gln) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000874 in 1,601,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000083 ( 0 hom. )

Consequence

RASGRP4
NM_170604.3 missense, splice_region

Scores

3
16
Splicing: ADA: 0.0002085
2

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.161
Variant links:
Genes affected
RASGRP4 (HGNC:18958): (RAS guanyl releasing protein 4) The protein encoded by this gene is a member of the Ras guanyl nucleotide-releasing protein (RasGRP) family of Ras guanine nucleotide exchange factors. It contains a Ras exchange motif, a diacylglycerol-binding domain, and two calcium-binding EF hands. This protein was shown to activate H-Ras in a cation-dependent manner in vitro. Expression of this protein in myeloid cell lines was found to be correlated with elevated level of activated RAS protein, and the RAS activation can be greatly enhanced by phorbol ester treatment, which suggested a role of this protein in diacylglycerol regulated cell signaling pathways. Studies of a mast cell leukemia cell line expressing substantial amounts of abnormal transcripts of this gene indicated that this gene may play an important role in the final stages of mast cell development. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2009]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.21924457).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RASGRP4NM_170604.3 linkc.1715G>A p.Arg572Gln missense_variant, splice_region_variant Exon 14 of 17 ENST00000615439.5 NP_733749.1 Q8TDF6-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RASGRP4ENST00000615439.5 linkc.1715G>A p.Arg572Gln missense_variant, splice_region_variant Exon 14 of 17 1 NM_170604.3 ENSP00000479844.1 Q8TDF6-1
RASGRP4ENST00000587738.2 linkc.1715G>A p.Arg572Gln missense_variant, splice_region_variant Exon 14 of 17 5 ENSP00000465772.1 Q8TDF6-1
RASGRP4ENST00000586305.5 linkc.1673G>A p.Arg558Gln missense_variant, splice_region_variant Exon 14 of 17 1 ENSP00000467604.1 Q8TDF6-2
RASGRP4ENST00000454404.6 linkc.1613G>A p.Arg538Gln missense_variant, splice_region_variant Exon 14 of 17 1 ENSP00000416463.2 Q8TDF6-8
RASGRP4ENST00000587753.5 linkc.1508G>A p.Arg503Gln missense_variant, splice_region_variant Exon 14 of 17 1 ENSP00000468483.1 Q8TDF6-9
RASGRP4ENST00000614135.4 linkc.1439G>A p.Arg480Gln missense_variant, splice_region_variant Exon 13 of 16 5 ENSP00000479078.1 Q8TDF6-5
RASGRP4ENST00000617966.4 linkc.1424G>A p.Arg475Gln missense_variant, splice_region_variant Exon 12 of 15 5 ENSP00000479888.1 Q8TDF6-7
RASGRP4ENST00000622174.4 linkc.1148G>A p.Arg383Gln missense_variant, splice_region_variant Exon 11 of 14 5 ENSP00000484345.1 Q8TDF6-6
RASGRP4ENST00000589358.5 linkn.1715G>A splice_region_variant, non_coding_transcript_exon_variant Exon 14 of 18 5 ENSP00000465742.1 Q8TDF6-1
RASGRP4ENST00000589474.5 linkn.1673G>A splice_region_variant, non_coding_transcript_exon_variant Exon 14 of 18 5 ENSP00000466928.1 Q8TDF6-2

Frequencies

GnomAD3 genomes
AF:
0.0000131
AC:
2
AN:
152170
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000828
AC:
12
AN:
1448998
Hom.:
0
Cov.:
32
AF XY:
0.00000278
AC XY:
2
AN XY:
719532
show subpopulations
Gnomad4 AFR exome
AF:
0.0000302
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000119
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000723
Gnomad4 OTH exome
AF:
0.0000334
GnomAD4 genome
AF:
0.0000131
AC:
2
AN:
152170
Hom.:
0
Cov.:
32
AF XY:
0.0000135
AC XY:
1
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Oct 17, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1715G>A (p.R572Q) alteration is located in exon 14 (coding exon 14) of the RASGRP4 gene. This alteration results from a G to A substitution at nucleotide position 1715, causing the arginine (R) at amino acid position 572 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.068
BayesDel_addAF
Benign
-0.0018
T
BayesDel_noAF
Benign
-0.24
CADD
Benign
18
DANN
Uncertain
1.0
DEOGEN2
Benign
0.039
.;.;.;.;.;.;T;.;.;T;.;T
Eigen
Benign
-0.27
Eigen_PC
Benign
-0.14
FATHMM_MKL
Benign
0.47
N
LIST_S2
Benign
0.84
.;.;.;T;D;.;T;D;D;D;D;.
M_CAP
Benign
0.036
D
MetaRNN
Benign
0.22
T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Uncertain
0.065
D
MutationAssessor
Benign
-0.19
.;.;.;.;.;.;.;.;.;N;.;N
PrimateAI
Benign
0.24
T
PROVEAN
Benign
-2.0
.;.;.;.;.;.;.;N;N;.;N;.
REVEL
Benign
0.18
Sift
Benign
0.059
.;.;.;.;.;.;.;T;T;.;T;.
Sift4G
Uncertain
0.019
D;D;D;D;D;D;D;D;D;D;D;D
Polyphen
0.010
B;.;.;.;.;.;.;.;.;B;.;B
Vest4
0.23
MutPred
0.26
.;.;.;.;.;.;Gain of sheet (P = 0.0827);.;.;Gain of sheet (P = 0.0827);.;Gain of sheet (P = 0.0827);
MVP
0.82
MPC
0.35
ClinPred
0.63
D
GERP RS
2.4
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.10
gMVP
0.24

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.00021
dbscSNV1_RF
Benign
0.20
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: rs776295355; hg19: chr19-38901987; API