NM_170604.3:c.1000G>T

Variant names:

• chr19-38415078-C-A
• rs762299166
• NM_170604.3:c.1000G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_170604.3(RASGRP4):​c.1000G>T​(p.Ala334Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,448,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A334T) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: RASGRP4 NM_170604.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.044361264).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RASGRP4	NM_170604.3	c.1000G>T	p.Ala334Ser	missense_variant	Exon 9 of 17	ENST00000615439.5	NP_733749.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RASGRP4	ENST00000615439.5	c.1000G>T	p.Ala334Ser	missense_variant	Exon 9 of 17	1	NM_170604.3	ENSP00000479844.1
RASGRP4	ENST00000587738.2	c.1000G>T	p.Ala334Ser	missense_variant	Exon 9 of 17	5		ENSP00000465772.1
RASGRP4	ENST00000586305.5	c.958G>T	p.Ala320Ser	missense_variant	Exon 9 of 17	1		ENSP00000467604.1
RASGRP4	ENST00000454404.6	c.898G>T	p.Ala300Ser	missense_variant	Exon 9 of 17	1		ENSP00000416463.2
RASGRP4	ENST00000617966.4	c.709G>T	p.Ala237Ser	missense_variant	Exon 7 of 15	5		ENSP00000479888.1
RASGRP4	ENST00000589358.5	n.1000G>T		non_coding_transcript_exon_variant	Exon 9 of 18	5		ENSP00000465742.1
RASGRP4	ENST00000589474.5	n.958G>T		non_coding_transcript_exon_variant	Exon 9 of 18	5		ENSP00000466928.1
RASGRP4	ENST00000587753.5	c.955-162G>T		intron_variant	Intron 8 of 16	1		ENSP00000468483.1
RASGRP4	ENST00000614135.4	c.955-1604G>T		intron_variant	Intron 8 of 15	5		ENSP00000479078.1
RASGRP4	ENST00000622174.4	c.664-1604G>T		intron_variant	Intron 6 of 13	5		ENSP00000484345.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000138 AC: 2 AN: 1448892 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 719426

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 33236

American (AMR) AF: 0.00 AC: 0 AN: 42762

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25810

East Asian (EAS) AF: 0.00 AC: 0 AN: 39224

South Asian (SAS) AF: 0.00 AC: 0 AN: 84698

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52048

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5256

European-Non Finnish (NFE) AF: 0.00000181 AC: 2 AN: 1106064

Other (OTH) AF: 0.00 AC: 0 AN: 59794

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00000000770867), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.079
BayesDel_addAF	Benign	-0.26	T
BayesDel_noAF	Benign	-0.61
CADD	Benign	9.0
DANN	Uncertain	0.98
DEOGEN2	Benign	0.0079	.;.;.;T;.;T;T
Eigen	Benign	-0.74
Eigen_PC	Benign	-0.70
FATHMM_MKL	Benign	0.19	N
LIST_S2	Benign	0.67	.;T;.;T;T;T;.
M_CAP	Benign	0.0031	T
MetaRNN	Benign	0.044	T;T;T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	-0.21	.;.;.;.;.;N;N
PhyloP100		-0.074
PrimateAI	Benign	0.39	T
PROVEAN	Benign	0.28	.;.;.;.;N;.;.
REVEL	Benign	0.064
Sift	Benign	0.57	.;.;.;.;T;.;.
Sift4G	Benign	0.85	T;T;T;T;T;T;T
Polyphen		0.21	B;.;.;.;.;D;D
Vest4		0.064
MutPred		0.35		.;.;.;Gain of disorder (P = 0.0452);.;Gain of disorder (P = 0.0452);Gain of disorder (P = 0.0452);
MVP		0.11
MPC		0.33
ClinPred		0.10	T
GERP RS		2.5
Varity_R		0.18
gMVP		0.080
Mutation Taster		=82/18	polymorphism

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

Other links and lift over

dbSNP: rs762299166; hg19: chr19-38905718;