chr11-32057675-C-T

Variant summary

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

The ENST00000532942.5(ENSG00000285283):​c.102-39469C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,128 control chromosomes in the GnomAD database, including 3,260 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 ( 3260 hom., cov: 32)

Consequence

ENSG00000285283
ENST00000532942.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.338

Publications

5 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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 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
ENSG00000285283ENST00000532942.5 linkc.102-39469C>T intron_variant Intron 1 of 5 2 ENSP00000436422.1
ENSG00000285283ENST00000530348.5 linkc.-244-39469C>T intron_variant Intron 1 of 3 4 ENSP00000436482.1 E9PP27

Frequencies

GnomAD3 genomes
AF:
0.186
AC:
28287
AN:
152010
Hom.:
3257
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0514
Gnomad AMI
AF:
0.350
Gnomad AMR
AF:
0.259
Gnomad ASJ
AF:
0.170
Gnomad EAS
AF:
0.418
Gnomad SAS
AF:
0.258
Gnomad FIN
AF:
0.197
Gnomad MID
AF:
0.177
Gnomad NFE
AF:
0.225
Gnomad OTH
AF:
0.199
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.186
AC:
28294
AN:
152128
Hom.:
3260
Cov.:
32
AF XY:
0.188
AC XY:
13942
AN XY:
74352
show subpopulations
African (AFR)
AF:
0.0513
AC:
2131
AN:
41514
American (AMR)
AF:
0.259
AC:
3964
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.170
AC:
588
AN:
3464
East Asian (EAS)
AF:
0.419
AC:
2162
AN:
5166
South Asian (SAS)
AF:
0.257
AC:
1238
AN:
4812
European-Finnish (FIN)
AF:
0.197
AC:
2080
AN:
10576
Middle Eastern (MID)
AF:
0.184
AC:
54
AN:
294
European-Non Finnish (NFE)
AF:
0.225
AC:
15328
AN:
67986
Other (OTH)
AF:
0.203
AC:
430
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1125
2250
3376
4501
5626
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
314
628
942
1256
1570
<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:
0.202
Hom.:
7204
Bravo
AF:
0.188
Asia WGS
AF:
0.301
AC:
1043
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.7
DANN
Benign
0.62
PhyloP100
-0.34
Mutation Taster
=100/0
polymorphism (auto)

Splicing

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

Publications

Other links and lift over

dbSNP: rs12420599; hg19: chr11-32079221; API