rs3742717

chr14-92652323-C-Gchr14-92652323-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_024832.5(RIN3):c.1274C>G(p.Thr425Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 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. T425I) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 30)
• Consequence: RIN3 NM_024832.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211

Genes affected

RIN3 (HGNC:18751): (Ras and Rab interactor 3) Summary: This protein encoded by this gene is a member of the RIN family of Ras interaction-interference proteins, which are binding partners to the RAB5 small GTPases. The protein functions as a guanine nucleotide exchange for RAB5B and RAB31. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.027048409).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RIN3	NM_024832.5	c.1274C>G	p.Thr425Arg	missense_variant	6/10	ENST00000216487.12
RIN3	NM_001319987.2	c.1049C>G	p.Thr350Arg	missense_variant	5/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RIN3	ENST00000216487.12	c.1274C>G	p.Thr425Arg	missense_variant	6/10	1	NM_024832.5	P2
RIN3	ENST00000555589.5	c.*721C>G		3_prime_UTR_variant, NMD_transcript_variant	5/9	1
RIN3	ENST00000620541.4	c.1058C>G	p.Thr353Arg	missense_variant	7/11	5		A2
RIN3	ENST00000418924.6	n.1173C>G		non_coding_transcript_exon_variant	5/9	2

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 49

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.059
BayesDel_addAF	Benign	-0.41	T
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.60
Dann	Benign	0.55
DEOGEN2	Benign	0.00065	T;T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.013	N
LIST_S2	Benign	0.39	T;T
M_CAP	Benign	0.0040	T
MetaRNN	Benign	0.027	T;T
MetaSVM	Benign	-0.91	T
MutationAssessor	Benign	-1.4	N;.
MutationTaster	Benign	1.0	P
PrimateAI	Benign	0.24	T
PROVEAN	Benign	0.30	N;.
REVEL	Benign	0.025
Sift	Benign	0.26	T;.
Sift4G	Benign	0.59	T;T
Polyphen		0.0010	B;.
Vest4		0.044
MutPred		0.12		Loss of phosphorylation at T425 (P = 0.0028);.;
MVP		0.16
MPC		0.30
ClinPred		0.054	T
GERP RS		-0.54
Varity_R		0.024
gMVP		0.14

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: rs3742717; hg19: chr14-93118668;