rs7301722

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 0.339 in 151,648 control chromosomes in the GnomAD database, including 8,602 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 0.34 ( 8602 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.18

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=-0.79).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 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:
0.339
AC:
51354
AN:
151534
Hom.:
8585
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.360
Gnomad AMI
AF:
0.372
Gnomad AMR
AF:
0.323
Gnomad ASJ
AF:
0.339
Gnomad EAS
AF:
0.291
Gnomad SAS
AF:
0.237
Gnomad FIN
AF:
0.426
Gnomad MID
AF:
0.268
Gnomad NFE
AF:
0.328
Gnomad OTH
AF:
0.325
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.339
AC:
51403
AN:
151648
Hom.:
8602
Cov.:
32
AF XY:
0.340
AC XY:
25211
AN XY:
74066
show subpopulations
African (AFR)
AF:
0.360
AC:
14886
AN:
41358
American (AMR)
AF:
0.323
AC:
4924
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.339
AC:
1170
AN:
3454
East Asian (EAS)
AF:
0.292
AC:
1494
AN:
5124
South Asian (SAS)
AF:
0.237
AC:
1141
AN:
4814
European-Finnish (FIN)
AF:
0.426
AC:
4467
AN:
10496
Middle Eastern (MID)
AF:
0.257
AC:
75
AN:
292
European-Non Finnish (NFE)
AF:
0.328
AC:
22216
AN:
67834
Other (OTH)
AF:
0.330
AC:
695
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.495
Heterozygous variant carriers
0
1718
3436
5154
6872
8590
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
506
1012
1518
2024
2530
<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:
0.334
Hom.:
1066
Bravo
AF:
0.334
Asia WGS
AF:
0.272
AC:
946
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
3.4
DANN
Benign
0.67
PhyloP100
-2.2

Splicing

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

Publications

Other links and lift over

dbSNP: rs7301722; hg19: chr12-131356055; COSMIC: COSV54562615; API