rs7705033

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 0.324 in 151,920 control chromosomes in the GnomAD database, including 8,242 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 0.32 ( 8242 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0490

Publications

9 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 = 0.391 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:
0.324
AC:
49136
AN:
151802
Hom.:
8208
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.395
Gnomad AMI
AF:
0.183
Gnomad AMR
AF:
0.323
Gnomad ASJ
AF:
0.206
Gnomad EAS
AF:
0.394
Gnomad SAS
AF:
0.383
Gnomad FIN
AF:
0.329
Gnomad MID
AF:
0.252
Gnomad NFE
AF:
0.278
Gnomad OTH
AF:
0.317
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.324
AC:
49212
AN:
151920
Hom.:
8242
Cov.:
32
AF XY:
0.326
AC XY:
24183
AN XY:
74234
show subpopulations
African (AFR)
AF:
0.396
AC:
16391
AN:
41402
American (AMR)
AF:
0.323
AC:
4930
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.206
AC:
716
AN:
3472
East Asian (EAS)
AF:
0.394
AC:
2036
AN:
5174
South Asian (SAS)
AF:
0.382
AC:
1832
AN:
4800
European-Finnish (FIN)
AF:
0.329
AC:
3475
AN:
10548
Middle Eastern (MID)
AF:
0.247
AC:
72
AN:
292
European-Non Finnish (NFE)
AF:
0.278
AC:
18910
AN:
67940
Other (OTH)
AF:
0.323
AC:
683
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1638
3276
4914
6552
8190
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
502
1004
1506
2008
2510
<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:
0.267
Hom.:
3129
Bravo
AF:
0.323
Asia WGS
AF:
0.465
AC:
1614
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
4.7
DANN
Benign
0.61
PhyloP100
-0.049

Splicing

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

Publications

Other links and lift over

dbSNP: rs7705033; hg19: chr5-122774785; API