rs174479

Variant names:

• chr11-61911282-C-G
• rs174479
• NM_013401.4:c.12-2976G>C

Variant summary

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

The NM_013401.4(RAB3IL1):​c.12-2976G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,170 control chromosomes in the GnomAD database, including 2,599 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 0.17 (2599 hom., cov: 32)
• Consequence: RAB3IL1 NM_013401.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 24 publications found

Genes affected

RAB3IL1 (HGNC:9780): (RAB3A interacting protein like 1) This gene encodes a guanine nucleotide exchange factor for the ras-related protein Rab3A. The encoded protein binds Rab3a and the inositol hexakisphosphate kinase InsP6K1. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 7. [provided by RefSeq, Nov 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013401.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB3IL1	NM_013401.4	MANE Select	c.12-2976G>C		intron	N/A	NP_037533.2
	RAB3IL1	NM_001271686.2		c.153-2976G>C		intron	N/A	NP_001258615.1	Q8TBN0-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB3IL1	ENST00000394836.7	TSL:1 MANE Select	c.12-2976G>C		intron	N/A	ENSP00000378313.2	Q8TBN0-1
	RAB3IL1	ENST00000301773.9	TSL:1	c.153-2976G>C		intron	N/A	ENSP00000301773.5	Q8TBN0-2
	RAB3IL1	ENST00000531922.2	TSL:3	c.153-2976G>C		intron	N/A	ENSP00000435444.2	E9PK89

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26449 AN: 152052 Hom.: 2601 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.0950

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.174 AC: 26441 AN: 152170 Hom.: 2599 Cov.: 32 AF XY: 0.175 AC XY: 13023 AN XY: 74382

African (AFR) AF: 0.166 AC: 6911 AN: 41530

American (AMR) AF: 0.180 AC: 2759 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0963 AC: 334 AN: 3468

East Asian (EAS) AF: 0.336 AC: 1730 AN: 5152

South Asian (SAS) AF: 0.407 AC: 1959 AN: 4818

European-Finnish (FIN) AF: 0.0950 AC: 1006 AN: 10590

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11240 AN: 67992

Other (OTH) AF: 0.175 AC: 371 AN: 2114

Alfa AF: 0.159 Hom.: 248

Bravo AF: 0.178

Asia WGS AF: 0.362 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.6
DANN	Benign	0.80
PhyloP100		-0.096
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: rs174479; hg19: chr11-61678754;