rs878854761

chr11-534319-T-Achr11-534319-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM1 PM2 BP4

The NM_005343.4(HRAS):c.4A>T(p.Thr2Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 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. T2A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 34)
• Consequence: HRAS NM_005343.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.87

Genes affected

HRAS (HGNC:5173): (HRas proto-oncogene, GTPase) This gene belongs to the Ras oncogene family, whose members are related to the transforming genes of mammalian sarcoma retroviruses. The products encoded by these genes function in signal transduction pathways. These proteins can bind GTP and GDP, and they have intrinsic GTPase activity. This protein undergoes a continuous cycle of de- and re-palmitoylation, which regulates its rapid exchange between the plasma membrane and the Golgi apparatus. Mutations in this gene cause Costello syndrome, a disease characterized by increased growth at the prenatal stage, growth deficiency at the postnatal stage, predisposition to tumor formation, cognitive disability, skin and musculoskeletal abnormalities, distinctive facial appearance and cardiovascular abnormalities. Defects in this gene are implicated in a variety of cancers, including bladder cancer, follicular thyroid cancer, and oral squamous cell carcinoma. Multiple transcript variants, which encode different isoforms, have been identified for this gene. [provided by RefSeq, Jul 2008]

LRRC56 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM1: In a modified_residue N-acetylthreonine; in GTPase HRas, N-terminally processed (size 0) in uniprot entity RASH_HUMAN
• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.27935433).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HRAS	NM_005343.4	c.4A>T	p.Thr2Ser	missense_variant	2/6	ENST00000311189.8
HRAS	NM_176795.5	c.4A>T	p.Thr2Ser	missense_variant	2/6	ENST00000417302.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HRAS	ENST00000311189.8	c.4A>T	p.Thr2Ser	missense_variant	2/6	1	NM_005343.4	P1
HRAS	ENST00000417302.7	c.4A>T	p.Thr2Ser	missense_variant	2/6	5	NM_176795.5

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.42
BayesDel_addAF	Benign	-0.0037	T
BayesDel_noAF	Benign	-0.24
Cadd	Benign	22
Dann	Benign	0.93
Eigen	Benign	-0.43
Eigen_PC	Benign	-0.30
FATHMM_MKL	Pathogenic	0.98	D
M_CAP	Benign	0.065	D
MetaRNN	Benign	0.28	T;T;T;T;T
MetaSVM	Benign	-0.91	T
MutationAssessor	Benign	-0.17	N;N;N;N;N
MutationTaster	Benign	1.0	D;D;D;D;D
PrimateAI	Pathogenic	0.80	T
PROVEAN	Benign	-2.0	N;N;N;N;N
REVEL	Benign	0.26
Sift	Benign	0.15	T;T;T;T;T
Sift4G	Benign	0.74	T;T;T;T;T
Polyphen		0.010	B;B;B;B;B
Vest4		0.27
MutPred		0.26		Gain of disorder (P = 0.0593);Gain of disorder (P = 0.0593);Gain of disorder (P = 0.0593);Gain of disorder (P = 0.0593);Gain of disorder (P = 0.0593);
MVP		0.87
MPC		0.95
ClinPred		0.58	D
GERP RS		3.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.52
gMVP		0.66

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-534319;