19-38411201-T-C

Variant names:

• chr19-38411201-T-C
• rs1971240066
• NM_170604.3:c.1766A>G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_170604.3(RASGRP4):​c.1766A>G​(p.Glu589Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,666 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: RASGRP4 NM_170604.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.12

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RASGRP4	NM_170604.3	c.1766A>G	p.Glu589Gly	missense_variant	Exon 15 of 17	ENST00000615439.5	NP_733749.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RASGRP4	ENST00000615439.5	c.1766A>G	p.Glu589Gly	missense_variant	Exon 15 of 17	1	NM_170604.3	ENSP00000479844.1
RASGRP4	ENST00000587738.2	c.1766A>G	p.Glu589Gly	missense_variant	Exon 15 of 17	5		ENSP00000465772.1
RASGRP4	ENST00000586305.5	c.1724A>G	p.Glu575Gly	missense_variant	Exon 15 of 17	1		ENSP00000467604.1
RASGRP4	ENST00000454404.6	c.1664A>G	p.Glu555Gly	missense_variant	Exon 15 of 17	1		ENSP00000416463.2
RASGRP4	ENST00000587753.5	c.1559A>G	p.Glu520Gly	missense_variant	Exon 15 of 17	1		ENSP00000468483.1
RASGRP4	ENST00000614135.4	c.1490A>G	p.Glu497Gly	missense_variant	Exon 14 of 16	5		ENSP00000479078.1
RASGRP4	ENST00000617966.4	c.1475A>G	p.Glu492Gly	missense_variant	Exon 13 of 15	5		ENSP00000479888.1
RASGRP4	ENST00000622174.4	c.1199A>G	p.Glu400Gly	missense_variant	Exon 12 of 14	5		ENSP00000484345.1
RASGRP4	ENST00000589358.5	n.1766A>G		non_coding_transcript_exon_variant	Exon 15 of 18	5		ENSP00000465742.1
RASGRP4	ENST00000589474.5	n.1724A>G		non_coding_transcript_exon_variant	Exon 15 of 18	5		ENSP00000466928.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461666 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 727116

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Dec 20, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1766A>G (p.E589G) alteration is located in exon 15 (coding exon 15) of the RASGRP4 gene. This alteration results from a A to G substitution at nucleotide position 1766, causing the glutamic acid (E) at amino acid position 589 to be replaced by a glycine (G). 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	0.21
BayesDel_addAF	Pathogenic	0.32	D
BayesDel_noAF	Pathogenic	0.22
CADD	Pathogenic	27
DANN	Pathogenic	1.0
DEOGEN2	Uncertain	0.76	.;.;.;.;.;.;.;.;D;.;D
Eigen	Uncertain	0.53
Eigen_PC	Uncertain	0.47
FATHMM_MKL	Uncertain	0.86	D
LIST_S2	Uncertain	0.92	.;.;.;D;D;.;D;D;D;D;.
M_CAP	Uncertain	0.27	D
MetaRNN	Uncertain	0.72	D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	0.91	D
MutationAssessor	Uncertain	2.6	.;.;.;.;.;.;.;.;M;.;M
PrimateAI	Benign	0.47	T
PROVEAN	Pathogenic	-5.6	.;.;.;.;.;.;D;D;.;D;.
REVEL	Pathogenic	0.71
Sift	Uncertain	0.0010	.;.;.;.;.;.;D;D;.;D;.
Sift4G	Uncertain	0.016	D;D;D;D;D;D;D;D;D;D;D
Polyphen		0.99	D;.;.;.;.;.;.;.;D;.;D
Vest4		0.58
MutPred		0.50		.;.;.;.;.;.;.;.;Gain of MoRF binding (P = 0.0256);.;Gain of MoRF binding (P = 0.0256);
MVP		0.83
MPC		1.1
ClinPred		0.99	D
GERP RS		5.8
Varity_R		0.57
gMVP		0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.28		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.28		Position offset: 5

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1971240066; hg19: chr19-38901841;