chr15-39281334-A-G

Variant summary

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

The ENST00000558209.1(ENSG00000259345):​n.451+78455T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,102 control chromosomes in the GnomAD database, including 3,414 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 0.19 ( 3414 hom., cov: 32)

Consequence

ENSG00000259345
ENST00000558209.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.549

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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105370777XR_007064588.1 linkn.517+139210T>C intron_variant Intron 1 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000259345ENST00000558209.1 linkn.451+78455T>C intron_variant Intron 2 of 2 3
ENSG00000259345ENST00000560484.1 linkn.67+139575T>C intron_variant Intron 1 of 3 4

Frequencies

GnomAD3 genomes
AF:
0.187
AC:
28456
AN:
151984
Hom.:
3410
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.349
Gnomad AMI
AF:
0.149
Gnomad AMR
AF:
0.108
Gnomad ASJ
AF:
0.136
Gnomad EAS
AF:
0.0100
Gnomad SAS
AF:
0.0951
Gnomad FIN
AF:
0.158
Gnomad MID
AF:
0.142
Gnomad NFE
AF:
0.136
Gnomad OTH
AF:
0.162
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.187
AC:
28492
AN:
152102
Hom.:
3414
Cov.:
32
AF XY:
0.183
AC XY:
13595
AN XY:
74358
show subpopulations
African (AFR)
AF:
0.349
AC:
14453
AN:
41454
American (AMR)
AF:
0.108
AC:
1644
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.136
AC:
470
AN:
3468
East Asian (EAS)
AF:
0.0102
AC:
53
AN:
5184
South Asian (SAS)
AF:
0.0940
AC:
453
AN:
4820
European-Finnish (FIN)
AF:
0.158
AC:
1669
AN:
10576
Middle Eastern (MID)
AF:
0.150
AC:
44
AN:
294
European-Non Finnish (NFE)
AF:
0.136
AC:
9229
AN:
68004
Other (OTH)
AF:
0.162
AC:
342
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1107
2213
3320
4426
5533
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
276
552
828
1104
1380
<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:
0.147
Hom.:
2877
Bravo
AF:
0.193
Asia WGS
AF:
0.0550
AC:
191
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.84
DANN
Benign
0.71
PhyloP100
-0.55

Splicing

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

Publications

Other links and lift over

dbSNP: rs12595668; hg19: chr15-39573535; API