rs17783660

Variant names:

• chr14-92595108-A-G
• rs17783660
• NM_024832.5:c.367+17631A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024832.5(RIN3):​c.367+17631A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0944 in 152,292 control chromosomes in the GnomAD database, including 802 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 0.094 (802 hom., cov: 33)
• Consequence: RIN3 NM_024832.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024832.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIN3	NM_024832.5	MANE Select	c.367+17631A>G		intron	N/A	NP_079108.3
	RIN3	NM_001319987.2		c.142+17631A>G		intron	N/A	NP_001306916.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIN3	ENST00000216487.12	TSL:1 MANE Select	c.367+17631A>G		intron	N/A	ENSP00000216487.7
	RIN3	ENST00000555589.5	TSL:1	n.367+17631A>G		intron	N/A	ENSP00000450682.1
	RIN3	ENST00000620541.4	TSL:5	c.367+17631A>G		intron	N/A	ENSP00000480603.1

Frequencies

GnomAD3 genomes AF: 0.0945 AC: 14383 AN: 152174 Hom.: 803 Cov.: 33

Gnomad AFR AF: 0.0574

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.00442

Gnomad SAS AF: 0.0327

Gnomad FIN AF: 0.0858

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0944 AC: 14382 AN: 152292 Hom.: 802 Cov.: 33 AF XY: 0.0910 AC XY: 6780 AN XY: 74476

African (AFR) AF: 0.0572 AC: 2378 AN: 41564

American (AMR) AF: 0.107 AC: 1637 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3472

East Asian (EAS) AF: 0.00443 AC: 23 AN: 5190

South Asian (SAS) AF: 0.0327 AC: 158 AN: 4830

European-Finnish (FIN) AF: 0.0858 AC: 909 AN: 10600

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8474 AN: 68012

Other (OTH) AF: 0.0990 AC: 209 AN: 2112

Alfa AF: 0.112 Hom.: 1021

Bravo AF: 0.0984

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.45
PhyloP100		-0.17
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: rs17783660; hg19: chr14-93061453;