11-61944003-T-G

Variant names:

• chr11-61944003-T-G
• rs2521572
• XM_011545197.3:c.29+1770A>C

Variant summary

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

The XM_011545197.3(RAB3IL1):​c.29+1770A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.905 in 152,260 control chromosomes in the GnomAD database, including 63,133 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 0.91 (63133 hom., cov: 31)
• Consequence: RAB3IL1 XM_011545197.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 18 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.905 AC: 137697 AN: 152142 Hom.: 63086 Cov.: 31

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.979

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.976

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.959

Gnomad OTH AF: 0.905

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

GnomAD4 genome AF: 0.905 AC: 137803 AN: 152260 Hom.: 63133 Cov.: 31 AF XY: 0.900 AC XY: 67044 AN XY: 74462

African (AFR) AF: 0.872 AC: 36194 AN: 41526

American (AMR) AF: 0.860 AC: 13148 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.979 AC: 3397 AN: 3470

East Asian (EAS) AF: 0.436 AC: 2257 AN: 5178

South Asian (SAS) AF: 0.856 AC: 4133 AN: 4826

European-Finnish (FIN) AF: 0.976 AC: 10373 AN: 10626

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.959 AC: 65219 AN: 68022

Other (OTH) AF: 0.907 AC: 1915 AN: 2112

Alfa AF: 0.935 Hom.: 266464

Bravo AF: 0.889

Asia WGS AF: 0.738 AC: 2567 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	2.6
DANN	Benign	0.78
PhyloP100		0.023

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2521572; hg19: chr11-61711475;