rs7286472

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 0.182 in 152,128 control chromosomes in the GnomAD database, including 3,279 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 0.18 ( 3279 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.317

Publications

5 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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 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:
0.182
AC:
27599
AN:
152010
Hom.:
3265
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.336
Gnomad AMI
AF:
0.146
Gnomad AMR
AF:
0.122
Gnomad ASJ
AF:
0.131
Gnomad EAS
AF:
0.0135
Gnomad SAS
AF:
0.0775
Gnomad FIN
AF:
0.114
Gnomad MID
AF:
0.190
Gnomad NFE
AF:
0.135
Gnomad OTH
AF:
0.171
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.182
AC:
27637
AN:
152128
Hom.:
3279
Cov.:
32
AF XY:
0.176
AC XY:
13120
AN XY:
74374
show subpopulations
African (AFR)
AF:
0.336
AC:
13919
AN:
41450
American (AMR)
AF:
0.122
AC:
1864
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
0.131
AC:
456
AN:
3472
East Asian (EAS)
AF:
0.0137
AC:
71
AN:
5178
South Asian (SAS)
AF:
0.0767
AC:
370
AN:
4824
European-Finnish (FIN)
AF:
0.114
AC:
1208
AN:
10596
Middle Eastern (MID)
AF:
0.187
AC:
55
AN:
294
European-Non Finnish (NFE)
AF:
0.135
AC:
9202
AN:
68002
Other (OTH)
AF:
0.170
AC:
359
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1090
2179
3269
4358
5448
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
276
552
828
1104
1380
<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:
0.146
Hom.:
3544
Bravo
AF:
0.188
Asia WGS
AF:
0.0800
AC:
282
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
4.2
DANN
Benign
0.72
PhyloP100
0.32

Splicing

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

Publications

Other links and lift over

dbSNP: rs7286472; hg19: chr22-34386473; API