chr17-15396028-A-G

Variant summary

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

The ENST00000580422.1(ENSG00000266667):​n.315-13907T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.935 in 152,050 control chromosomes in the GnomAD database, including 66,737 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 0.94 ( 66737 hom., cov: 30)

Consequence

ENSG00000266667
ENST00000580422.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0420

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=-0.94).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.969 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
ENSG00000266667ENST00000580422.1 linkn.315-13907T>C intron_variant Intron 2 of 3 5
ENSG00000266667ENST00000762561.1 linkn.325-13395T>C intron_variant Intron 2 of 2
ENSG00000266667ENST00000762562.1 linkn.292-13504T>C intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.936
AC:
142138
AN:
151932
Hom.:
66696
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.861
Gnomad AMI
AF:
0.963
Gnomad AMR
AF:
0.954
Gnomad ASJ
AF:
0.933
Gnomad EAS
AF:
0.905
Gnomad SAS
AF:
0.901
Gnomad FIN
AF:
0.973
Gnomad MID
AF:
0.937
Gnomad NFE
AF:
0.975
Gnomad OTH
AF:
0.941
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.935
AC:
142235
AN:
152050
Hom.:
66737
Cov.:
30
AF XY:
0.935
AC XY:
69497
AN XY:
74316
show subpopulations
African (AFR)
AF:
0.860
AC:
35633
AN:
41412
American (AMR)
AF:
0.954
AC:
14581
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.933
AC:
3239
AN:
3472
East Asian (EAS)
AF:
0.906
AC:
4653
AN:
5134
South Asian (SAS)
AF:
0.900
AC:
4334
AN:
4814
European-Finnish (FIN)
AF:
0.973
AC:
10297
AN:
10580
Middle Eastern (MID)
AF:
0.932
AC:
274
AN:
294
European-Non Finnish (NFE)
AF:
0.975
AC:
66360
AN:
68038
Other (OTH)
AF:
0.942
AC:
1988
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
433
867
1300
1734
2167
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
908
1816
2724
3632
4540
<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:
0.959
Hom.:
78141
Bravo
AF:
0.930
Asia WGS
AF:
0.897
AC:
3121
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
2.2
DANN
Benign
0.45
PhyloP100
0.042

Splicing

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

Publications

Other links and lift over

dbSNP: rs2024158; hg19: chr17-15299345; API