GeneBe

rs730012

Variant names:

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 0.283 in 985,288 control chromosomes in the GnomAD database, including 41,327 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 0.22 ( 4362 hom., cov: 33)
Exomes 𝑓: 0.29 ( 36965 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.63

Publications

118 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=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 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:
0.218
AC:
33120
AN:
152064
Hom.:
4363
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0829
Gnomad AMI
AF:
0.154
Gnomad AMR
AF:
0.179
Gnomad ASJ
AF:
0.239
Gnomad EAS
AF:
0.165
Gnomad SAS
AF:
0.186
Gnomad FIN
AF:
0.332
Gnomad MID
AF:
0.228
Gnomad NFE
AF:
0.297
Gnomad OTH
AF:
0.228
GnomAD4 exome
AF:
0.295
AC:
245618
AN:
833108
Hom.:
36965
Cov.:
32
AF XY:
0.294
AC XY:
113239
AN XY:
384714
show subpopulations
African (AFR)
AF:
0.0613
AC:
967
AN:
15786
American (AMR)
AF:
0.203
AC:
200
AN:
984
Ashkenazi Jewish (ASJ)
AF:
0.240
AC:
1234
AN:
5152
East Asian (EAS)
AF:
0.163
AC:
592
AN:
3630
South Asian (SAS)
AF:
0.189
AC:
3110
AN:
16460
European-Finnish (FIN)
AF:
0.283
AC:
78
AN:
276
Middle Eastern (MID)
AF:
0.229
AC:
371
AN:
1620
European-Non Finnish (NFE)
AF:
0.304
AC:
231871
AN:
761902
Other (OTH)
AF:
0.264
AC:
7195
AN:
27298
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.487
Heterozygous variant carriers
0
10800
21600
32401
43201
54001
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
10314
20628
30942
41256
51570
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.218
AC:
33129
AN:
152180
Hom.:
4362
Cov.:
33
AF XY:
0.217
AC XY:
16173
AN XY:
74414
show subpopulations
African (AFR)
AF:
0.0829
AC:
3443
AN:
41544
American (AMR)
AF:
0.179
AC:
2738
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.239
AC:
830
AN:
3470
East Asian (EAS)
AF:
0.165
AC:
854
AN:
5176
South Asian (SAS)
AF:
0.188
AC:
907
AN:
4826
European-Finnish (FIN)
AF:
0.332
AC:
3523
AN:
10598
Middle Eastern (MID)
AF:
0.214
AC:
63
AN:
294
European-Non Finnish (NFE)
AF:
0.297
AC:
20157
AN:
67966
Other (OTH)
AF:
0.225
AC:
474
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1287
2574
3862
5149
6436
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
350
700
1050
1400
1750
<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:
0.264
Hom.:
10342
Bravo
AF:
0.200
Asia WGS
AF:
0.165
AC:
573
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.0040
DANN
Benign
0.70
PhyloP100
-3.6
PromoterAI
-0.042
Neutral
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs730012; hg19: chr5-179220638; API