chr18-78675166-G-A

Variant summary

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

The ENST00000759065.1(ENSG00000298930):​n.186-3316C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 150,192 control chromosomes in the GnomAD database, including 10,017 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 ( 10017 hom., cov: 29)

Consequence

ENSG00000298930
ENST00000759065.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.421

Publications

1 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=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.625 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
ENSG00000298930ENST00000759065.1 linkn.186-3316C>T intron_variant Intron 1 of 4

Frequencies

GnomAD3 genomes
AF:
0.331
AC:
49735
AN:
150080
Hom.:
10014
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.0900
Gnomad AMI
AF:
0.406
Gnomad AMR
AF:
0.390
Gnomad ASJ
AF:
0.314
Gnomad EAS
AF:
0.642
Gnomad SAS
AF:
0.476
Gnomad FIN
AF:
0.496
Gnomad MID
AF:
0.362
Gnomad NFE
AF:
0.403
Gnomad OTH
AF:
0.351
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.331
AC:
49731
AN:
150192
Hom.:
10017
Cov.:
29
AF XY:
0.340
AC XY:
24897
AN XY:
73236
show subpopulations
African (AFR)
AF:
0.0898
AC:
3642
AN:
40562
American (AMR)
AF:
0.390
AC:
5901
AN:
15132
Ashkenazi Jewish (ASJ)
AF:
0.314
AC:
1090
AN:
3466
East Asian (EAS)
AF:
0.643
AC:
3273
AN:
5090
South Asian (SAS)
AF:
0.474
AC:
2236
AN:
4714
European-Finnish (FIN)
AF:
0.496
AC:
5077
AN:
10246
Middle Eastern (MID)
AF:
0.366
AC:
106
AN:
290
European-Non Finnish (NFE)
AF:
0.403
AC:
27295
AN:
67698
Other (OTH)
AF:
0.356
AC:
743
AN:
2088
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.534
Heterozygous variant carriers
0
1518
3036
4553
6071
7589
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
490
980
1470
1960
2450
<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.:
18266
Bravo
AF:
0.310
Asia WGS
AF:
0.541
AC:
1878
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
3.0
DANN
Benign
0.46
PhyloP100
-0.42

Splicing

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

Publications

Other links and lift over

dbSNP: rs12605652; hg19: chr18-76435166; API