rs16993280
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The variant allele was found at a frequency of 0.146 in 151,166 control chromosomes in the GnomAD database, including 1,871 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 0.15 ( 1870 hom., cov: 31)
Exomes 𝑓: 0.11 ( 1 hom. )
Consequence
IGL
intragenic
intragenic
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.273
Publications
4 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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IGL | n.22814988G>A | intragenic_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000289120 | ENST00000686504.1 | n.208+3395C>T | intron_variant | Intron 2 of 3 | ||||||
ENSG00000289120 | ENST00000702002.1 | n.207+3395C>T | intron_variant | Intron 2 of 2 | ||||||
ENSG00000226477 | ENST00000423259.1 | n.*62G>A | downstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes AF: 0.146 AC: 22001AN: 150882Hom.: 1871 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
22001
AN:
150882
Hom.:
Cov.:
31
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:
GnomAD4 exome AF: 0.111 AC: 20AN: 180Hom.: 1 AF XY: 0.0956 AC XY: 13AN XY: 136 show subpopulations
GnomAD4 exome
AF:
AC:
20
AN:
180
Hom.:
AF XY:
AC XY:
13
AN XY:
136
show subpopulations
African (AFR)
AF:
AC:
0
AN:
4
American (AMR)
AF:
AC:
0
AN:
2
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
6
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AF:
AC:
1
AN:
4
European-Finnish (FIN)
AF:
AC:
5
AN:
14
Middle Eastern (MID)
AF:
AC:
0
AN:
6
European-Non Finnish (NFE)
AF:
AC:
14
AN:
132
Other (OTH)
AF:
AC:
0
AN:
12
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.492
Heterozygous variant carriers
0
2
3
5
6
8
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<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: 0.146 AC: 22006AN: 150986Hom.: 1870 Cov.: 31 AF XY: 0.142 AC XY: 10462AN XY: 73704 show subpopulations
GnomAD4 genome
AF:
AC:
22006
AN:
150986
Hom.:
Cov.:
31
AF XY:
AC XY:
10462
AN XY:
73704
show subpopulations
African (AFR)
AF:
AC:
8964
AN:
41096
American (AMR)
AF:
AC:
1443
AN:
15114
Ashkenazi Jewish (ASJ)
AF:
AC:
438
AN:
3464
East Asian (EAS)
AF:
AC:
3
AN:
4914
South Asian (SAS)
AF:
AC:
215
AN:
4754
European-Finnish (FIN)
AF:
AC:
1533
AN:
10552
Middle Eastern (MID)
AF:
AC:
37
AN:
264
European-Non Finnish (NFE)
AF:
AC:
8872
AN:
67836
Other (OTH)
AF:
AC:
270
AN:
2086
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
879
1757
2636
3514
4393
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
236
472
708
944
1180
<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:
123
AN:
3466
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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