2-226732872-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005544.3(IRS1):​c.*3400T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,112 control chromosomes in the GnomAD database, including 1,204 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 0.10 ( 1204 hom., cov: 32)
Exomes 𝑓: 0.083 ( 0 hom. )

Consequence

IRS1
NM_005544.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.87
Variant links:
Genes affected
IRS1 (HGNC:6125): (insulin receptor substrate 1) This gene encodes a protein which is phosphorylated by insulin receptor tyrosine kinase. Mutations in this gene are associated with type II diabetes and susceptibility to insulin resistance. [provided by RefSeq, Nov 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IRS1NM_005544.3 linkuse as main transcriptc.*3400T>C 3_prime_UTR_variant 2/2 ENST00000305123.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IRS1ENST00000305123.6 linkuse as main transcriptc.*3400T>C 3_prime_UTR_variant 2/21 NM_005544.3 P1

Frequencies

GnomAD3 genomes
AF:
0.104
AC:
15773
AN:
151982
Hom.:
1199
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.193
Gnomad AMI
AF:
0.0848
Gnomad AMR
AF:
0.135
Gnomad ASJ
AF:
0.0937
Gnomad EAS
AF:
0.188
Gnomad SAS
AF:
0.140
Gnomad FIN
AF:
0.0175
Gnomad MID
AF:
0.0854
Gnomad NFE
AF:
0.0484
Gnomad OTH
AF:
0.0895
GnomAD4 exome
AF:
0.0833
AC:
1
AN:
12
Hom.:
0
Cov.:
0
AF XY:
0.125
AC XY:
1
AN XY:
8
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.125
GnomAD4 genome
AF:
0.104
AC:
15814
AN:
152100
Hom.:
1204
Cov.:
32
AF XY:
0.104
AC XY:
7720
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.193
Gnomad4 AMR
AF:
0.135
Gnomad4 ASJ
AF:
0.0937
Gnomad4 EAS
AF:
0.188
Gnomad4 SAS
AF:
0.140
Gnomad4 FIN
AF:
0.0175
Gnomad4 NFE
AF:
0.0485
Gnomad4 OTH
AF:
0.0885
Alfa
AF:
0.0840
Hom.:
161
Bravo
AF:
0.120
Asia WGS
AF:
0.150
AC:
519
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.16
DANN
Benign
0.29

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

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

Other links and lift over

dbSNP: rs13431554; hg19: chr2-227597588; API