rs1113000

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 0.25 in 151,952 control chromosomes in the GnomAD database, including 4,857 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 0.25 ( 4857 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.23

Publications

1 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 (AMR) allele frequency at 95% confidence interval = 0.283 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:
0.250
AC:
38032
AN:
151834
Hom.:
4866
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.237
Gnomad AMI
AF:
0.347
Gnomad AMR
AF:
0.291
Gnomad ASJ
AF:
0.338
Gnomad EAS
AF:
0.289
Gnomad SAS
AF:
0.241
Gnomad FIN
AF:
0.231
Gnomad MID
AF:
0.334
Gnomad NFE
AF:
0.244
Gnomad OTH
AF:
0.264
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.250
AC:
38035
AN:
151952
Hom.:
4857
Cov.:
31
AF XY:
0.250
AC XY:
18546
AN XY:
74250
show subpopulations
African (AFR)
AF:
0.237
AC:
9814
AN:
41452
American (AMR)
AF:
0.291
AC:
4433
AN:
15256
Ashkenazi Jewish (ASJ)
AF:
0.338
AC:
1174
AN:
3472
East Asian (EAS)
AF:
0.289
AC:
1495
AN:
5172
South Asian (SAS)
AF:
0.241
AC:
1160
AN:
4814
European-Finnish (FIN)
AF:
0.231
AC:
2438
AN:
10540
Middle Eastern (MID)
AF:
0.336
AC:
98
AN:
292
European-Non Finnish (NFE)
AF:
0.244
AC:
16554
AN:
67940
Other (OTH)
AF:
0.263
AC:
553
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1458
2915
4373
5830
7288
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
396
792
1188
1584
1980
<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:
0.253
Hom.:
1748
Bravo
AF:
0.258
Asia WGS
AF:
0.265
AC:
921
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
0.26
DANN
Benign
0.70
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: rs1113000; hg19: chr14-63133404; API