chr12-53865917-G-A

Variant summary

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

The ENST00000652339.1(ENSG00000286069):​n.509+5039G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,974 control chromosomes in the GnomAD database, including 10,041 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 0.36 ( 10041 hom., cov: 31)

Consequence

ENSG00000286069
ENST00000652339.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.07

Publications

3 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=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105378250NR_189097.1 linkn.398+15505G>A intron_variant Intron 2 of 2
LOC105378250NR_189098.1 linkn.497-9238G>A intron_variant Intron 3 of 4
LOC105378250NR_189099.1 linkn.591+5039G>A intron_variant Intron 4 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000286069ENST00000652339.1 linkn.509+5039G>A intron_variant Intron 4 of 4
ENSG00000286069ENST00000654713.2 linkn.317+15505G>A intron_variant Intron 2 of 2
ENSG00000286069ENST00000656247.1 linkn.344+15505G>A intron_variant Intron 3 of 3

Frequencies

GnomAD3 genomes
AF:
0.358
AC:
54440
AN:
151856
Hom.:
10039
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.333
Gnomad AMI
AF:
0.404
Gnomad AMR
AF:
0.262
Gnomad ASJ
AF:
0.420
Gnomad EAS
AF:
0.229
Gnomad SAS
AF:
0.359
Gnomad FIN
AF:
0.320
Gnomad MID
AF:
0.304
Gnomad NFE
AF:
0.408
Gnomad OTH
AF:
0.338
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.358
AC:
54451
AN:
151974
Hom.:
10041
Cov.:
31
AF XY:
0.351
AC XY:
26099
AN XY:
74294
show subpopulations
African (AFR)
AF:
0.333
AC:
13794
AN:
41444
American (AMR)
AF:
0.262
AC:
3995
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
0.420
AC:
1459
AN:
3470
East Asian (EAS)
AF:
0.230
AC:
1184
AN:
5158
South Asian (SAS)
AF:
0.359
AC:
1728
AN:
4820
European-Finnish (FIN)
AF:
0.320
AC:
3377
AN:
10554
Middle Eastern (MID)
AF:
0.313
AC:
92
AN:
294
European-Non Finnish (NFE)
AF:
0.408
AC:
27744
AN:
67954
Other (OTH)
AF:
0.337
AC:
712
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1765
3530
5295
7060
8825
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
536
1072
1608
2144
2680
<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:
0.283
Hom.:
1035
Bravo
AF:
0.350
Asia WGS
AF:
0.288
AC:
1008
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
6.9
DANN
Benign
0.39
PhyloP100
1.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs7306498; hg19: chr12-54259701; API