rs1120038

Variant summary

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

The ENST00000661853.1(ENSG00000287704):​n.46-94491A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 151,850 control chromosomes in the GnomAD database, including 7,562 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 0.31 ( 7562 hom., cov: 31)

Consequence

ENSG00000287704
ENST00000661853.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.49

Publications

0 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 (AMR) allele frequency at 95% confidence interval = 0.355 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
ENSG00000287704ENST00000661853.1 linkn.46-94491A>G intron_variant Intron 1 of 1
ENSG00000287704ENST00000686120.1 linkn.57-12483A>G intron_variant Intron 1 of 2
ENSG00000287704ENST00000736459.1 linkn.47-12483A>G intron_variant Intron 1 of 3
ENSG00000287704ENST00000736460.1 linkn.39-12483A>G intron_variant Intron 1 of 4

Frequencies

GnomAD3 genomes
AF:
0.312
AC:
47276
AN:
151732
Hom.:
7558
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.232
Gnomad AMI
AF:
0.531
Gnomad AMR
AF:
0.363
Gnomad ASJ
AF:
0.369
Gnomad EAS
AF:
0.159
Gnomad SAS
AF:
0.218
Gnomad FIN
AF:
0.315
Gnomad MID
AF:
0.405
Gnomad NFE
AF:
0.358
Gnomad OTH
AF:
0.378
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.311
AC:
47297
AN:
151850
Hom.:
7562
Cov.:
31
AF XY:
0.309
AC XY:
22925
AN XY:
74208
show subpopulations
African (AFR)
AF:
0.232
AC:
9634
AN:
41444
American (AMR)
AF:
0.363
AC:
5534
AN:
15256
Ashkenazi Jewish (ASJ)
AF:
0.369
AC:
1278
AN:
3468
East Asian (EAS)
AF:
0.159
AC:
817
AN:
5136
South Asian (SAS)
AF:
0.218
AC:
1050
AN:
4810
European-Finnish (FIN)
AF:
0.315
AC:
3321
AN:
10546
Middle Eastern (MID)
AF:
0.405
AC:
119
AN:
294
European-Non Finnish (NFE)
AF:
0.358
AC:
24269
AN:
67880
Other (OTH)
AF:
0.376
AC:
793
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.496
Heterozygous variant carriers
0
1637
3273
4910
6546
8183
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
462
924
1386
1848
2310
<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:
0.328
Hom.:
1024
Bravo
AF:
0.317
Asia WGS
AF:
0.199
AC:
691
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
0.88
DANN
Benign
0.75
PhyloP100
-1.5

Splicing

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

Publications

Other links and lift over

dbSNP: rs1120038; hg19: chr15-46857922; API