NM_006764.5:c.-121T>C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006764.5(IFRD2):c.-121T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 1,586,248 control chromosomes in the GnomAD database, including 391,136 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 0.77 ( 46402 hom., cov: 35)
Exomes 𝑓: 0.69 ( 344734 hom. )
Consequence
IFRD2
NM_006764.5 5_prime_UTR
NM_006764.5 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.226
Publications
31 publications found
Genes affected
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.770 AC: 117196AN: 152126Hom.: 46340 Cov.: 35 show subpopulations
GnomAD3 genomes
AF:
AC:
117196
AN:
152126
Hom.:
Cov.:
35
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.712 AC: 144573AN: 203022 AF XY: 0.691 show subpopulations
GnomAD2 exomes
AF:
AC:
144573
AN:
203022
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.690 AC: 989121AN: 1434006Hom.: 344734 Cov.: 74 AF XY: 0.683 AC XY: 487014AN XY: 712626 show subpopulations
GnomAD4 exome
AF:
AC:
989121
AN:
1434006
Hom.:
Cov.:
74
AF XY:
AC XY:
487014
AN XY:
712626
show subpopulations
African (AFR)
AF:
AC:
31397
AN:
32926
American (AMR)
AF:
AC:
35975
AN:
41878
Ashkenazi Jewish (ASJ)
AF:
AC:
19338
AN:
25668
East Asian (EAS)
AF:
AC:
29038
AN:
38488
South Asian (SAS)
AF:
AC:
42941
AN:
84158
European-Finnish (FIN)
AF:
AC:
28149
AN:
41242
Middle Eastern (MID)
AF:
AC:
3995
AN:
5742
European-Non Finnish (NFE)
AF:
AC:
755790
AN:
1104268
Other (OTH)
AF:
AC:
42498
AN:
59636
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.484
Heterozygous variant carriers
0
19632
39263
58895
78526
98158
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
19432
38864
58296
77728
97160
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.771 AC: 117314AN: 152242Hom.: 46402 Cov.: 35 AF XY: 0.766 AC XY: 57005AN XY: 74418 show subpopulations
GnomAD4 genome
AF:
AC:
117314
AN:
152242
Hom.:
Cov.:
35
AF XY:
AC XY:
57005
AN XY:
74418
show subpopulations
African (AFR)
AF:
AC:
39317
AN:
41578
American (AMR)
AF:
AC:
12739
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
AC:
2611
AN:
3472
East Asian (EAS)
AF:
AC:
3968
AN:
5160
South Asian (SAS)
AF:
AC:
2402
AN:
4828
European-Finnish (FIN)
AF:
AC:
7322
AN:
10596
Middle Eastern (MID)
AF:
AC:
215
AN:
292
European-Non Finnish (NFE)
AF:
AC:
46439
AN:
67996
Other (OTH)
AF:
AC:
1630
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1357
2713
4070
5426
6783
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
842
1684
2526
3368
4210
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2166
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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