15-48108002-A-G

Variant summary

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

The ENST00000730753.1(ENSG00000295542):​n.65-613A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,158 control chromosomes in the GnomAD database, including 15,691 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 0.28 ( 15691 hom., cov: 32)

Consequence

ENSG00000295542
ENST00000730753.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07

Publications

24 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 (AFR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC124903485XR_007064619.1 linkn.183-1105T>C intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000295542ENST00000730753.1 linkn.65-613A>G intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.280
AC:
42646
AN:
152040
Hom.:
15616
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.796
Gnomad AMI
AF:
0.0296
Gnomad AMR
AF:
0.266
Gnomad ASJ
AF:
0.00144
Gnomad EAS
AF:
0.735
Gnomad SAS
AF:
0.216
Gnomad FIN
AF:
0.00424
Gnomad MID
AF:
0.0255
Gnomad NFE
AF:
0.00407
Gnomad OTH
AF:
0.214
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.281
AC:
42791
AN:
152158
Hom.:
15691
Cov.:
32
AF XY:
0.281
AC XY:
20880
AN XY:
74420
show subpopulations
African (AFR)
AF:
0.797
AC:
33042
AN:
41458
American (AMR)
AF:
0.267
AC:
4087
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
0.00144
AC:
5
AN:
3470
East Asian (EAS)
AF:
0.735
AC:
3795
AN:
5164
South Asian (SAS)
AF:
0.214
AC:
1032
AN:
4826
European-Finnish (FIN)
AF:
0.00424
AC:
45
AN:
10620
Middle Eastern (MID)
AF:
0.0274
AC:
8
AN:
292
European-Non Finnish (NFE)
AF:
0.00407
AC:
277
AN:
68006
Other (OTH)
AF:
0.224
AC:
473
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
589
1177
1766
2354
2943
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
306
612
918
1224
1530
<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:
0.383
Hom.:
8606
Bravo
AF:
0.328
Asia WGS
AF:
0.567
AC:
1969
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
0.49
DANN
Benign
0.38
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: rs2675345; hg19: chr15-48400199; API