GeneBe

21-14259866-C-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000429114.5(ABCC13):​n.102-8537C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,092 control chromosomes in the GnomAD database, including 20,436 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 0.52 ( 20436 hom., cov: 33)

Consequence

ABCC13
ENST00000429114.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04

Publications

2 publications found
Variant links:
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=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ABCC13ENST00000429114.5 linkn.102-8537C>G intron_variant Intron 1 of 4 3

Frequencies

GnomAD3 genomes
AF:
0.516
AC:
78370
AN:
151974
Hom.:
20426
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.433
Gnomad AMI
AF:
0.634
Gnomad AMR
AF:
0.486
Gnomad ASJ
AF:
0.597
Gnomad EAS
AF:
0.581
Gnomad SAS
AF:
0.579
Gnomad FIN
AF:
0.537
Gnomad MID
AF:
0.589
Gnomad NFE
AF:
0.553
Gnomad OTH
AF:
0.538
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.516
AC:
78404
AN:
152092
Hom.:
20436
Cov.:
33
AF XY:
0.516
AC XY:
38394
AN XY:
74340
show subpopulations
African (AFR)
AF:
0.432
AC:
17924
AN:
41470
American (AMR)
AF:
0.486
AC:
7427
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
0.597
AC:
2070
AN:
3468
East Asian (EAS)
AF:
0.581
AC:
3009
AN:
5176
South Asian (SAS)
AF:
0.577
AC:
2786
AN:
4826
European-Finnish (FIN)
AF:
0.537
AC:
5672
AN:
10572
Middle Eastern (MID)
AF:
0.592
AC:
174
AN:
294
European-Non Finnish (NFE)
AF:
0.553
AC:
37618
AN:
67980
Other (OTH)
AF:
0.543
AC:
1146
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1969
3937
5906
7874
9843
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
688
1376
2064
2752
3440
<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:
0.373
Hom.:
947
Bravo
AF:
0.510
Asia WGS
AF:
0.599
AC:
2085
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.46
DANN
Benign
0.71
PhyloP100
-1.0

Splicing

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

Publications

Other links and lift over

dbSNP: rs432114; hg19: chr21-15632187; API