rs6682554
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_138346.3(KIAA2013):c.-327A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,566 control chromosomes in the GnomAD database, including 25,941 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 0.58 ( 25925 hom., cov: 29)
Exomes 𝑓: 0.56 ( 16 hom. )
Consequence
KIAA2013
NM_138346.3 upstream_gene
NM_138346.3 upstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.76
Publications
13 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=-0.83).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.580 AC: 87862AN: 151362Hom.: 25885 Cov.: 29 show subpopulations
GnomAD3 genomes
AF:
AC:
87862
AN:
151362
Hom.:
Cov.:
29
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: 0.561 AC: 46AN: 82Hom.: 16 AF XY: 0.559 AC XY: 38AN XY: 68 show subpopulations
GnomAD4 exome
AF:
AC:
46
AN:
82
Hom.:
AF XY:
AC XY:
38
AN XY:
68
show subpopulations
African (AFR)
AF:
AC:
3
AN:
4
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
AC:
1
AN:
2
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
5
AN:
6
Middle Eastern (MID)
AF:
AC:
0
AN:
2
European-Non Finnish (NFE)
AF:
AC:
36
AN:
64
Other (OTH)
AF:
AC:
1
AN:
4
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.521
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.581 AC: 87970AN: 151484Hom.: 25925 Cov.: 29 AF XY: 0.583 AC XY: 43109AN XY: 73966 show subpopulations
GnomAD4 genome
AF:
AC:
87970
AN:
151484
Hom.:
Cov.:
29
AF XY:
AC XY:
43109
AN XY:
73966
show subpopulations
African (AFR)
AF:
AC:
26686
AN:
41308
American (AMR)
AF:
AC:
7611
AN:
15254
Ashkenazi Jewish (ASJ)
AF:
AC:
1585
AN:
3468
East Asian (EAS)
AF:
AC:
3286
AN:
5072
South Asian (SAS)
AF:
AC:
3201
AN:
4810
European-Finnish (FIN)
AF:
AC:
6619
AN:
10450
Middle Eastern (MID)
AF:
AC:
134
AN:
294
European-Non Finnish (NFE)
AF:
AC:
37373
AN:
67824
Other (OTH)
AF:
AC:
1196
AN:
2100
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.512
Heterozygous variant carriers
0
1808
3615
5423
7230
9038
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2379
AN:
3476
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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