3-87446400-C-T

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 0.145 in 151,842 control chromosomes in the GnomAD database, including 2,214 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 ( 2214 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.185

Publications

4 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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 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:
0.145
AC:
22007
AN:
151724
Hom.:
2207
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.293
Gnomad AMI
AF:
0.228
Gnomad AMR
AF:
0.0752
Gnomad ASJ
AF:
0.0652
Gnomad EAS
AF:
0.0874
Gnomad SAS
AF:
0.0929
Gnomad FIN
AF:
0.161
Gnomad MID
AF:
0.0478
Gnomad NFE
AF:
0.0809
Gnomad OTH
AF:
0.110
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.145
AC:
22035
AN:
151842
Hom.:
2214
Cov.:
31
AF XY:
0.146
AC XY:
10866
AN XY:
74194
show subpopulations
African (AFR)
AF:
0.293
AC:
12132
AN:
41376
American (AMR)
AF:
0.0751
AC:
1146
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.0652
AC:
226
AN:
3468
East Asian (EAS)
AF:
0.0877
AC:
454
AN:
5174
South Asian (SAS)
AF:
0.0919
AC:
443
AN:
4820
European-Finnish (FIN)
AF:
0.161
AC:
1689
AN:
10486
Middle Eastern (MID)
AF:
0.0445
AC:
13
AN:
292
European-Non Finnish (NFE)
AF:
0.0809
AC:
5495
AN:
67942
Other (OTH)
AF:
0.109
AC:
230
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
887
1774
2662
3549
4436
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
222
444
666
888
1110
<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:
0.0935
Hom.:
3882
Bravo
AF:
0.146
Asia WGS
AF:
0.0980
AC:
341
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
2.9
DANN
Benign
0.44
PhyloP100
0.18

Splicing

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

Publications

Other links and lift over

dbSNP: rs9834692; hg19: chr3-87495550; API