rs11042902

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PVS1_ModerateBA1

The ENST00000534266.6(IRAG1):​c.-670-2G>A variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 1,585,126 control chromosomes in the GnomAD database, including 66,537 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.25 ( 5378 hom., cov: 31)
Exomes 𝑓: 0.28 ( 61159 hom. )

Consequence

IRAG1
ENST00000534266.6 splice_acceptor, intron

Scores

2
Splicing: ADA: 0.06107
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0510
Variant links:
Genes affected
IRAG1 (HGNC:7237): (inositol 1,4,5-triphosphate receptor associated 1) This gene is similar to a putative mouse tumor suppressor gene (Mrvi1) that is frequently disrupted by mouse AIDS-related virus (MRV). The encoded protein, which is found in the membrane of the endoplasmic reticulum, is similar to Jaw1, a lymphoid-restricted protein whose expression is down-regulated during lymphoid differentiation. This protein is a substrate of cGMP-dependent kinase-1 (PKG1) that can function as a regulator of IP3-induced calcium release. Studies in mouse suggest that MRV integration at Mrvi1 induces myeloid leukemia by altering the expression of a gene important for myeloid cell growth and/or differentiation, and thus this gene may function as a myeloid leukemia tumor suppressor gene. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene, and alternative translation start sites, including a non-AUG (CUG) start site, are used. [provided by RefSeq, May 2011]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

PVS1
Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.059643254 fraction of the gene. Cryptic splice site detected, with MaxEntScore 5.6, offset of 0 (no position change), new splice context is: gtgtttttgttctaaaccAGcag. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IRAG1NM_130385.4 linkc.226-5G>A splice_region_variant, intron_variant Intron 2 of 20 ENST00000423302.7 NP_569056.4 Q9Y6F6-7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IRAG1ENST00000423302.7 linkc.226-5G>A splice_region_variant, intron_variant Intron 2 of 20 2 NM_130385.4 ENSP00000412130.2 Q9Y6F6-7
IRAG1ENST00000534266.6 linkc.-670-2G>A splice_acceptor_variant, intron_variant Intron 1 of 18 2 ENSP00000433296.2 Q9Y6F6-6
IRAG1ENST00000526414.5 linkn.70-2G>A splice_acceptor_variant, intron_variant Intron 2 of 16 2 ENSP00000435658.1 E9PJ61

Frequencies

GnomAD3 genomes
AF:
0.254
AC:
38581
AN:
151808
Hom.:
5380
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.194
Gnomad AMI
AF:
0.420
Gnomad AMR
AF:
0.213
Gnomad ASJ
AF:
0.306
Gnomad EAS
AF:
0.0201
Gnomad SAS
AF:
0.171
Gnomad FIN
AF:
0.341
Gnomad MID
AF:
0.304
Gnomad NFE
AF:
0.305
Gnomad OTH
AF:
0.249
GnomAD3 exomes
AF:
0.247
AC:
56221
AN:
227246
Hom.:
7863
AF XY:
0.249
AC XY:
30556
AN XY:
122616
show subpopulations
Gnomad AFR exome
AF:
0.199
Gnomad AMR exome
AF:
0.152
Gnomad ASJ exome
AF:
0.305
Gnomad EAS exome
AF:
0.0223
Gnomad SAS exome
AF:
0.159
Gnomad FIN exome
AF:
0.346
Gnomad NFE exome
AF:
0.317
Gnomad OTH exome
AF:
0.276
GnomAD4 exome
AF:
0.283
AC:
406074
AN:
1433200
Hom.:
61159
Cov.:
24
AF XY:
0.281
AC XY:
199911
AN XY:
712534
show subpopulations
Gnomad4 AFR exome
AF:
0.193
Gnomad4 AMR exome
AF:
0.158
Gnomad4 ASJ exome
AF:
0.304
Gnomad4 EAS exome
AF:
0.0115
Gnomad4 SAS exome
AF:
0.159
Gnomad4 FIN exome
AF:
0.338
Gnomad4 NFE exome
AF:
0.308
Gnomad4 OTH exome
AF:
0.268
GnomAD4 genome
AF:
0.254
AC:
38590
AN:
151926
Hom.:
5378
Cov.:
31
AF XY:
0.253
AC XY:
18771
AN XY:
74236
show subpopulations
Gnomad4 AFR
AF:
0.194
Gnomad4 AMR
AF:
0.213
Gnomad4 ASJ
AF:
0.306
Gnomad4 EAS
AF:
0.0200
Gnomad4 SAS
AF:
0.172
Gnomad4 FIN
AF:
0.341
Gnomad4 NFE
AF:
0.305
Gnomad4 OTH
AF:
0.250
Alfa
AF:
0.291
Hom.:
10301
Bravo
AF:
0.244
Asia WGS
AF:
0.103
AC:
359
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.71
CADD
Benign
4.3
DANN
Benign
0.79

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.061
dbscSNV1_RF
Benign
0.57
SpliceAI score (max)
0.97
Details are displayed if max score is > 0.2
DS_AG_spliceai
0.97
Position offset: -2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11042902; hg19: chr11-10655623; COSMIC: COSV70212057; COSMIC: COSV70212057; API