rs10896449

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 0.523 in 152,026 control chromosomes in the GnomAD database, including 22,269 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 0.52 ( 22269 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0260
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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 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:
0.523
AC:
79447
AN:
151908
Hom.:
22233
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.684
Gnomad AMI
AF:
0.416
Gnomad AMR
AF:
0.393
Gnomad ASJ
AF:
0.659
Gnomad EAS
AF:
0.0691
Gnomad SAS
AF:
0.329
Gnomad FIN
AF:
0.468
Gnomad MID
AF:
0.646
Gnomad NFE
AF:
0.505
Gnomad OTH
AF:
0.538
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.523
AC:
79536
AN:
152026
Hom.:
22269
Cov.:
32
AF XY:
0.515
AC XY:
38251
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.684
AC:
0.684254
AN:
0.684254
Gnomad4 AMR
AF:
0.392
AC:
0.391814
AN:
0.391814
Gnomad4 ASJ
AF:
0.659
AC:
0.65879
AN:
0.65879
Gnomad4 EAS
AF:
0.0683
AC:
0.068305
AN:
0.068305
Gnomad4 SAS
AF:
0.329
AC:
0.328631
AN:
0.328631
Gnomad4 FIN
AF:
0.468
AC:
0.468011
AN:
0.468011
Gnomad4 NFE
AF:
0.505
AC:
0.504886
AN:
0.504886
Gnomad4 OTH
AF:
0.536
AC:
0.536424
AN:
0.536424
Heterozygous variant carriers
0
1817
3634
5450
7267
9084
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
674
1348
2022
2696
3370
<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:
0.501
Hom.:
76080
Bravo
AF:
0.527
Asia WGS
AF:
0.298
AC:
1038
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
3.7
DANN
Benign
0.45

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10896449; hg19: chr11-68994667; API