chr1-161499264-G-C

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 0.491 in 151,780 control chromosomes in the GnomAD database, including 18,697 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 0.49 ( 18697 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.365

Publications

17 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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 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:
0.491
AC:
74432
AN:
151662
Hom.:
18696
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.529
Gnomad AMI
AF:
0.347
Gnomad AMR
AF:
0.433
Gnomad ASJ
AF:
0.420
Gnomad EAS
AF:
0.249
Gnomad SAS
AF:
0.406
Gnomad FIN
AF:
0.502
Gnomad MID
AF:
0.522
Gnomad NFE
AF:
0.509
Gnomad OTH
AF:
0.481
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.491
AC:
74474
AN:
151780
Hom.:
18697
Cov.:
31
AF XY:
0.486
AC XY:
36080
AN XY:
74174
show subpopulations
African (AFR)
AF:
0.529
AC:
21849
AN:
41340
American (AMR)
AF:
0.433
AC:
6605
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
0.420
AC:
1457
AN:
3468
East Asian (EAS)
AF:
0.250
AC:
1290
AN:
5170
South Asian (SAS)
AF:
0.405
AC:
1949
AN:
4808
European-Finnish (FIN)
AF:
0.502
AC:
5290
AN:
10528
Middle Eastern (MID)
AF:
0.524
AC:
154
AN:
294
European-Non Finnish (NFE)
AF:
0.509
AC:
34553
AN:
67900
Other (OTH)
AF:
0.481
AC:
1012
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1891
3781
5672
7562
9453
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
658
1316
1974
2632
3290
<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:
0.352
Hom.:
877
Bravo
AF:
0.491
Asia WGS
AF:
0.352
AC:
1226
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
11
DANN
Benign
0.76
PhyloP100
0.36

Splicing

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

Publications

Other links and lift over

dbSNP: rs6658353; hg19: chr1-161469054; API