rs11088655

Variant summary

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

The ENST00000813817.1(ENSG00000305890):​n.129+14558C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,992 control chromosomes in the GnomAD database, including 6,472 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 ( 6472 hom., cov: 33)

Consequence

ENSG00000305890
ENST00000813817.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.305

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=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC124900465XR_007067823.1 linkn.1606-55079C>T intron_variant Intron 2 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000305890ENST00000813817.1 linkn.129+14558C>T intron_variant Intron 1 of 1
ENSG00000305890ENST00000813818.1 linkn.194+14558C>T intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.275
AC:
41775
AN:
151874
Hom.:
6466
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.406
Gnomad AMI
AF:
0.249
Gnomad AMR
AF:
0.192
Gnomad ASJ
AF:
0.206
Gnomad EAS
AF:
0.0204
Gnomad SAS
AF:
0.186
Gnomad FIN
AF:
0.330
Gnomad MID
AF:
0.220
Gnomad NFE
AF:
0.236
Gnomad OTH
AF:
0.279
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.275
AC:
41810
AN:
151992
Hom.:
6472
Cov.:
33
AF XY:
0.276
AC XY:
20485
AN XY:
74310
show subpopulations
African (AFR)
AF:
0.406
AC:
16811
AN:
41456
American (AMR)
AF:
0.191
AC:
2919
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
0.206
AC:
714
AN:
3470
East Asian (EAS)
AF:
0.0207
AC:
107
AN:
5180
South Asian (SAS)
AF:
0.186
AC:
898
AN:
4818
European-Finnish (FIN)
AF:
0.330
AC:
3475
AN:
10542
Middle Eastern (MID)
AF:
0.219
AC:
64
AN:
292
European-Non Finnish (NFE)
AF:
0.236
AC:
16011
AN:
67952
Other (OTH)
AF:
0.277
AC:
584
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1506
3013
4519
6026
7532
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
414
828
1242
1656
2070
<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:
0.263
Hom.:
925
Bravo
AF:
0.269
Asia WGS
AF:
0.112
AC:
391
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
4.7
DANN
Benign
0.60
PhyloP100
0.30

Splicing

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

Publications

Other links and lift over

dbSNP: rs11088655; hg19: chr21-19206489; API