chr14-85754586-T-G

Variant summary

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

The variant allele was found at a frequency of 0.4 in 151,914 control chromosomes in the GnomAD database, including 13,006 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 0.40 ( 13006 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.814

Publications

3 publications found
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 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

Frequencies

GnomAD3 genomes
AF:
0.401
AC:
60829
AN:
151796
Hom.:
13010
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.265
Gnomad AMI
AF:
0.582
Gnomad AMR
AF:
0.395
Gnomad ASJ
AF:
0.452
Gnomad EAS
AF:
0.162
Gnomad SAS
AF:
0.326
Gnomad FIN
AF:
0.500
Gnomad MID
AF:
0.392
Gnomad NFE
AF:
0.487
Gnomad OTH
AF:
0.419
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.400
AC:
60839
AN:
151914
Hom.:
13006
Cov.:
31
AF XY:
0.399
AC XY:
29601
AN XY:
74238
show subpopulations
African (AFR)
AF:
0.265
AC:
10982
AN:
41482
American (AMR)
AF:
0.395
AC:
6013
AN:
15212
Ashkenazi Jewish (ASJ)
AF:
0.452
AC:
1567
AN:
3470
East Asian (EAS)
AF:
0.163
AC:
838
AN:
5144
South Asian (SAS)
AF:
0.326
AC:
1569
AN:
4818
European-Finnish (FIN)
AF:
0.500
AC:
5280
AN:
10562
Middle Eastern (MID)
AF:
0.388
AC:
114
AN:
294
European-Non Finnish (NFE)
AF:
0.487
AC:
33074
AN:
67920
Other (OTH)
AF:
0.415
AC:
875
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1793
3586
5379
7172
8965
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
570
1140
1710
2280
2850
<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:
0.438
Hom.:
2643
Bravo
AF:
0.389
Asia WGS
AF:
0.266
AC:
926
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.68
DANN
Benign
0.45
PhyloP100
-0.81

Splicing

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

Publications

Other links and lift over

dbSNP: rs12879941; hg19: chr14-86220930; API