chr18-60369270-G-A

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.113+39925G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,012 control chromosomes in the GnomAD database, including 8,780 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 0.33 ( 8780 hom., cov: 32)

Consequence

ENSG00000285681
ENST00000650201.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.84

Publications

12 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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 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
ENSG00000285681ENST00000650201.1 linkn.113+39925G>A intron_variant Intron 1 of 3
ENSG00000285681ENST00000658928.1 linkn.156+39925G>A intron_variant Intron 1 of 3

Frequencies

GnomAD3 genomes
AF:
0.327
AC:
49673
AN:
151894
Hom.:
8754
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.450
Gnomad AMI
AF:
0.373
Gnomad AMR
AF:
0.287
Gnomad ASJ
AF:
0.229
Gnomad EAS
AF:
0.127
Gnomad SAS
AF:
0.279
Gnomad FIN
AF:
0.216
Gnomad MID
AF:
0.247
Gnomad NFE
AF:
0.302
Gnomad OTH
AF:
0.317
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.327
AC:
49734
AN:
152012
Hom.:
8780
Cov.:
32
AF XY:
0.319
AC XY:
23705
AN XY:
74280
show subpopulations
African (AFR)
AF:
0.451
AC:
18672
AN:
41432
American (AMR)
AF:
0.286
AC:
4369
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.229
AC:
794
AN:
3470
East Asian (EAS)
AF:
0.127
AC:
655
AN:
5170
South Asian (SAS)
AF:
0.277
AC:
1336
AN:
4820
European-Finnish (FIN)
AF:
0.216
AC:
2285
AN:
10566
Middle Eastern (MID)
AF:
0.259
AC:
76
AN:
294
European-Non Finnish (NFE)
AF:
0.302
AC:
20543
AN:
67972
Other (OTH)
AF:
0.315
AC:
665
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.496
Heterozygous variant carriers
0
1648
3297
4945
6594
8242
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
494
988
1482
1976
2470
<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:
0.315
Hom.:
19531
Bravo
AF:
0.344
Asia WGS
AF:
0.209
AC:
728
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.023
DANN
Benign
0.23
PhyloP100
-1.8

Splicing

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

Publications

Other links and lift over

dbSNP: rs8093815; hg19: chr18-58036503; API