rs6682554

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.76

Publications

13 publications found
Variant links:
Genes affected
KIAA2013 (HGNC:28513): (KIAA2013) Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KIAA2013NM_138346.3 linkc.-327A>G upstream_gene_variant ENST00000376572.8 NP_612355.1 Q8IYS2-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KIAA2013ENST00000376572.8 linkc.-327A>G upstream_gene_variant 1 NM_138346.3 ENSP00000365756.3 Q8IYS2-1
KIAA2013ENST00000376576.3 linkc.-327A>G upstream_gene_variant 2 ENSP00000365760.3 Q8IYS2-2

Frequencies

GnomAD3 genomes
AF:
0.580
AC:
87862
AN:
151362
Hom.:
25885
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.646
Gnomad AMI
AF:
0.309
Gnomad AMR
AF:
0.498
Gnomad ASJ
AF:
0.457
Gnomad EAS
AF:
0.647
Gnomad SAS
AF:
0.666
Gnomad FIN
AF:
0.633
Gnomad MID
AF:
0.443
Gnomad NFE
AF:
0.551
Gnomad OTH
AF:
0.571
GnomAD4 exome
AF:
0.561
AC:
46
AN:
82
Hom.:
16
AF XY:
0.559
AC XY:
38
AN XY:
68
show subpopulations
African (AFR)
AF:
0.750
AC:
3
AN:
4
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
0.500
AC:
1
AN:
2
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.833
AC:
5
AN:
6
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2
European-Non Finnish (NFE)
AF:
0.563
AC:
36
AN:
64
Other (OTH)
AF:
0.250
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

Age Distribution

Exome Hom
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:
0.581
AC:
87970
AN:
151484
Hom.:
25925
Cov.:
29
AF XY:
0.583
AC XY:
43109
AN XY:
73966
show subpopulations
African (AFR)
AF:
0.646
AC:
26686
AN:
41308
American (AMR)
AF:
0.499
AC:
7611
AN:
15254
Ashkenazi Jewish (ASJ)
AF:
0.457
AC:
1585
AN:
3468
East Asian (EAS)
AF:
0.648
AC:
3286
AN:
5072
South Asian (SAS)
AF:
0.665
AC:
3201
AN:
4810
European-Finnish (FIN)
AF:
0.633
AC:
6619
AN:
10450
Middle Eastern (MID)
AF:
0.456
AC:
134
AN:
294
European-Non Finnish (NFE)
AF:
0.551
AC:
37373
AN:
67824
Other (OTH)
AF:
0.570
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

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
756
1512
2268
3024
3780
<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:
0.567
Hom.:
15490
Bravo
AF:
0.569
Asia WGS
AF:
0.685
AC:
2379
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.1
DANN
Benign
0.60
PhyloP100
-2.8
PromoterAI
-0.021
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs6682554; hg19: chr1-11986621; COSMIC: COSV105307854; API