GeneBe

rs1800776

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 0.0573 in 482,760 control chromosomes in the GnomAD database, including 1,005 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 0.055 ( 274 hom., cov: 33)
Exomes 𝑓: 0.059 ( 731 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.620

Publications

15 publications found
Variant links:

Genome browser will be placed here

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0737 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:
0.0547
AC:
8313
AN:
152090
Hom.:
273
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0324
Gnomad AMI
AF:
0.140
Gnomad AMR
AF:
0.0551
Gnomad ASJ
AF:
0.0611
Gnomad EAS
AF:
0.000770
Gnomad SAS
AF:
0.0315
Gnomad FIN
AF:
0.0301
Gnomad MID
AF:
0.161
Gnomad NFE
AF:
0.0754
Gnomad OTH
AF:
0.0646
GnomAD2 exomes
AF:
0.0520
AC:
9140
AN:
175874
AF XY:
0.0526
show subpopulations
Gnomad AFR exome
AF:
0.0287
Gnomad AMR exome
AF:
0.0463
Gnomad ASJ exome
AF:
0.0588
Gnomad EAS exome
AF:
0.000414
Gnomad FIN exome
AF:
0.0294
Gnomad NFE exome
AF:
0.0735
Gnomad OTH exome
AF:
0.0724
GnomAD4 exome
AF:
0.0586
AC:
19365
AN:
330552
Hom.:
731
Cov.:
0
AF XY:
0.0575
AC XY:
10853
AN XY:
188680
show subpopulations
African (AFR)
AF:
0.0303
AC:
296
AN:
9770
American (AMR)
AF:
0.0474
AC:
1489
AN:
31394
Ashkenazi Jewish (ASJ)
AF:
0.0608
AC:
679
AN:
11170
East Asian (EAS)
AF:
0.000337
AC:
4
AN:
11880
South Asian (SAS)
AF:
0.0329
AC:
2028
AN:
61666
European-Finnish (FIN)
AF:
0.0327
AC:
483
AN:
14778
Middle Eastern (MID)
AF:
0.125
AC:
348
AN:
2788
European-Non Finnish (NFE)
AF:
0.0757
AC:
13012
AN:
171854
Other (OTH)
AF:
0.0673
AC:
1026
AN:
15252
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.462
Heterozygous variant carriers
0
853
1707
2560
3414
4267
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
72
144
216
288
360
<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:
0.0546
AC:
8313
AN:
152208
Hom.:
274
Cov.:
33
AF XY:
0.0519
AC XY:
3865
AN XY:
74418
show subpopulations
African (AFR)
AF:
0.0323
AC:
1343
AN:
41528
American (AMR)
AF:
0.0549
AC:
839
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.0611
AC:
212
AN:
3470
East Asian (EAS)
AF:
0.000771
AC:
4
AN:
5186
South Asian (SAS)
AF:
0.0316
AC:
152
AN:
4814
European-Finnish (FIN)
AF:
0.0301
AC:
319
AN:
10604
Middle Eastern (MID)
AF:
0.177
AC:
52
AN:
294
European-Non Finnish (NFE)
AF:
0.0754
AC:
5130
AN:
68002
Other (OTH)
AF:
0.0634
AC:
134
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
400
800
1200
1600
2000
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
96
192
288
384
480
<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:
0.0539
Hom.:
117
Bravo
AF:
0.0571
Asia WGS
AF:
0.0190
AC:
66
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.2
DANN
Benign
0.71
PhyloP100
-0.62

Splicing

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

Publications

Other links and lift over

dbSNP: rs1800776; hg19: chr16-56995234; API