rs3018202

Variant names:

• chr18-42929162-A-G
• rs3018202
• NM_002930.4:c.235-5399T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RIT2	NM_002930.4	c.235-5399T>C		intron_variant	Intron 3 of 4	ENST00000326695.10	NP_002921.1
RIT2	NM_001272077.2	c.235-5399T>C		intron_variant	Intron 3 of 5		NP_001259006.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RIT2	ENST00000326695.10	c.235-5399T>C		intron_variant	Intron 3 of 4	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

African (AFR) AF: 0.272 AC: 11143 AN: 40988

American (AMR) AF: 0.265 AC: 3970 AN: 14994

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 430 AN: 3466

East Asian (EAS) AF: 0.339 AC: 1702 AN: 5018

South Asian (SAS) AF: 0.165 AC: 787 AN: 4756

European-Finnish (FIN) AF: 0.142 AC: 1441 AN: 10180

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 290

European-Non Finnish (NFE) AF: 0.0984 AC: 6666 AN: 67774

Other (OTH) AF: 0.143 AC: 298 AN: 2088

Alfa AF: 0.164 Hom.: 442

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
PhyloP100		1.5
Mutation Taster		=100/0	polymorphism (auto)

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: rs3018202; hg19: chr18-40509127;