chr5-136663359-G-A

Variant summary

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

The ENST00000718111.1(CTB-1I21.1):​n.309+62517G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0544 in 152,026 control chromosomes in the GnomAD database, including 505 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 0.054 ( 505 hom., cov: 33)

Consequence

CTB-1I21.1
ENST00000718111.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.608

Publications

1 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 (EAS) allele frequency at 95% confidence interval = 0.221 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
CTB-1I21.1ENST00000718111.1 linkn.309+62517G>A intron_variant Intron 2 of 3
CTB-1I21.1ENST00000755222.1 linkn.309+62517G>A intron_variant Intron 2 of 3
CTB-1I21.1ENST00000755223.1 linkn.309+62517G>A intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.0543
AC:
8251
AN:
151908
Hom.:
504
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.123
Gnomad AMI
AF:
0.0132
Gnomad AMR
AF:
0.0262
Gnomad ASJ
AF:
0.00922
Gnomad EAS
AF:
0.232
Gnomad SAS
AF:
0.108
Gnomad FIN
AF:
0.00910
Gnomad MID
AF:
0.0348
Gnomad NFE
AF:
0.0117
Gnomad OTH
AF:
0.0441
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0544
AC:
8269
AN:
152026
Hom.:
505
Cov.:
33
AF XY:
0.0557
AC XY:
4138
AN XY:
74314
show subpopulations
African (AFR)
AF:
0.123
AC:
5111
AN:
41456
American (AMR)
AF:
0.0261
AC:
399
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
0.00922
AC:
32
AN:
3470
East Asian (EAS)
AF:
0.232
AC:
1197
AN:
5162
South Asian (SAS)
AF:
0.109
AC:
522
AN:
4808
European-Finnish (FIN)
AF:
0.00910
AC:
96
AN:
10550
Middle Eastern (MID)
AF:
0.0306
AC:
9
AN:
294
European-Non Finnish (NFE)
AF:
0.0117
AC:
793
AN:
67994
Other (OTH)
AF:
0.0464
AC:
98
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
378
755
1133
1510
1888
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
102
204
306
408
510
<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:
0.0364
Hom.:
43
Bravo
AF:
0.0588
Asia WGS
AF:
0.148
AC:
513
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
7.5
DANN
Benign
0.57
PhyloP100
0.61

Splicing

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

Publications

Other links and lift over

dbSNP: rs2188468; hg19: chr5-135999048; API