chr11-121353175-G-C

Variant summary

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

The ENST00000761170.1(ENSG00000299150):​n.328+15474C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,014 control chromosomes in the GnomAD database, including 2,208 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 0.15 ( 2208 hom., cov: 31)

Consequence

ENSG00000299150
ENST00000761170.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.585

Publications

4 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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 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
ENSG00000299150ENST00000761170.1 linkn.328+15474C>G intron_variant Intron 1 of 2
ENSG00000299150ENST00000761171.1 linkn.216-15183C>G intron_variant Intron 1 of 4
ENSG00000299150ENST00000761172.1 linkn.197+15474C>G intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.154
AC:
23414
AN:
151896
Hom.:
2206
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.268
Gnomad AMI
AF:
0.0735
Gnomad AMR
AF:
0.148
Gnomad ASJ
AF:
0.0837
Gnomad EAS
AF:
0.166
Gnomad SAS
AF:
0.128
Gnomad FIN
AF:
0.103
Gnomad MID
AF:
0.104
Gnomad NFE
AF:
0.101
Gnomad OTH
AF:
0.136
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.154
AC:
23443
AN:
152014
Hom.:
2208
Cov.:
31
AF XY:
0.154
AC XY:
11415
AN XY:
74292
show subpopulations
African (AFR)
AF:
0.268
AC:
11117
AN:
41446
American (AMR)
AF:
0.148
AC:
2252
AN:
15254
Ashkenazi Jewish (ASJ)
AF:
0.0837
AC:
290
AN:
3466
East Asian (EAS)
AF:
0.166
AC:
857
AN:
5158
South Asian (SAS)
AF:
0.129
AC:
620
AN:
4824
European-Finnish (FIN)
AF:
0.103
AC:
1092
AN:
10576
Middle Eastern (MID)
AF:
0.112
AC:
33
AN:
294
European-Non Finnish (NFE)
AF:
0.100
AC:
6831
AN:
67974
Other (OTH)
AF:
0.135
AC:
284
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
956
1912
2867
3823
4779
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
236
472
708
944
1180
<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:
0.0423
Hom.:
32
Bravo
AF:
0.161
Asia WGS
AF:
0.149
AC:
518
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.78
DANN
Benign
0.70
PhyloP100
-0.58

Splicing

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

Publications

Other links and lift over

dbSNP: rs12286898; hg19: chr11-121223884; API