rs3018202

Positions:

• chr18-42929162-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002930.4(RIT2):​c.235-5399T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 150,456 control chromosomes in the GnomAD database, including 2,969 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 0.18 (2969 hom., cov: 28)
• Consequence: RIT2 NM_002930.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48

Genes affected

RIT2 (HGNC:10017): (Ras like without CAAX 2) RIN belongs to the RAS (HRAS; MIM 190020) superfamily of small GTPases (Shao et al., 1999 [PubMed 10545207]).[supplied by OMIM, Mar 2008]

RIT2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RIT2	NM_002930.4	c.235-5399T>C		intron_variant		ENST00000326695.10	NP_002921.1
RIT2	NM_001272077.2	c.235-5399T>C		intron_variant			NP_001259006.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RIT2	ENST00000326695.10	c.235-5399T>C		intron_variant		1	NM_002930.4	ENSP00000321805.4

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26632 AN: 150350 Hom.: 2962 Cov.: 28

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.0983

Gnomad OTH AF: 0.144

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.177 AC: 26664 AN: 150456 Hom.: 2969 Cov.: 28 AF XY: 0.180 AC XY: 13212 AN XY: 73434

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.0984

Gnomad4 OTH AF: 0.143

Alfa AF: 0.162 Hom.: 422

Bravo AF: 0.196

Asia WGS AF: 0.225 AC: 782 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.69

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

Other links and lift over

dbSNP: rs3018202; hg19: chr18-40509127;