chr15-46604485-C-T

Variant summary

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

The ENST00000661853.1(ENSG00000287704):​n.46-55730C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,046 control chromosomes in the GnomAD database, including 4,911 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 0.20 ( 4911 hom., cov: 32)

Consequence

ENSG00000287704
ENST00000661853.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.332

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=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 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.46-55730C>T intron_variant Intron 1 of 1
ENSG00000287704ENST00000686120.1 linkn.191+26144C>T intron_variant Intron 2 of 2
ENSG00000287704ENST00000736459.1 linkn.181+26144C>T intron_variant Intron 2 of 3

Frequencies

GnomAD3 genomes
AF:
0.199
AC:
30212
AN:
151928
Hom.:
4897
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.446
Gnomad AMI
AF:
0.0570
Gnomad AMR
AF:
0.110
Gnomad ASJ
AF:
0.104
Gnomad EAS
AF:
0.0214
Gnomad SAS
AF:
0.101
Gnomad FIN
AF:
0.0791
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.116
Gnomad OTH
AF:
0.175
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.199
AC:
30271
AN:
152046
Hom.:
4911
Cov.:
32
AF XY:
0.194
AC XY:
14401
AN XY:
74340
show subpopulations
African (AFR)
AF:
0.446
AC:
18488
AN:
41446
American (AMR)
AF:
0.110
AC:
1678
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
0.104
AC:
362
AN:
3472
East Asian (EAS)
AF:
0.0217
AC:
112
AN:
5166
South Asian (SAS)
AF:
0.101
AC:
489
AN:
4818
European-Finnish (FIN)
AF:
0.0791
AC:
838
AN:
10590
Middle Eastern (MID)
AF:
0.109
AC:
32
AN:
294
European-Non Finnish (NFE)
AF:
0.115
AC:
7851
AN:
67976
Other (OTH)
AF:
0.175
AC:
369
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1058
2116
3174
4232
5290
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
292
584
876
1168
1460
<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:
0.222
Hom.:
2875
Bravo
AF:
0.212
Asia WGS
AF:
0.106
AC:
368
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
2.3
DANN
Benign
0.35
PhyloP100
-0.33

Splicing

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

Publications

Other links and lift over

dbSNP: rs526439; hg19: chr15-46896683; API