rs4613156

Positions:

• chr18-42984220-G-C

Variant summary

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

The NM_002930.4(RIT2):​c.161-10073C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 151,928 control chromosomes in the GnomAD database, including 2,217 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 0.16 (2217 hom., cov: 33)
• Consequence: RIT2 NM_002930.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RIT2	NM_002930.4	c.161-10073C>G		intron_variant		ENST00000326695.10	NP_002921.1
RIT2	NM_001272077.2	c.161-10073C>G		intron_variant			NP_001259006.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RIT2	ENST00000326695.10	c.161-10073C>G		intron_variant		1	NM_002930.4	ENSP00000321805	P1
RIT2	ENST00000589109.5	c.161-10073C>G		intron_variant		1		ENSP00000467217
RIT2	ENST00000590910.1	c.161-10073C>G		intron_variant		5		ENSP00000466620
RIT2	ENST00000650392.1	c.161-10073C>G		intron_variant, NMD_transcript_variant				ENSP00000497708

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24833 AN: 151810 Hom.: 2207 Cov.: 33

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.00501

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.164 AC: 24864 AN: 151928 Hom.: 2217 Cov.: 33 AF XY: 0.165 AC XY: 12236 AN XY: 74272

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.00502

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.174

Alfa AF: 0.162 Hom.: 252

Bravo AF: 0.162

Asia WGS AF: 0.0970 AC: 337 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.14
DANN	Benign	0.28

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: rs4613156; hg19: chr18-40564185;