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GeneBe

rs10896449

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.523 in 151908 control chromosomes in the gnomAD Genomes database, including 22233 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 ( 22233 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0260

Links

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE 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
Alfa
AF:
0.504
Hom.:
31807
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
3.8
Dann
Benign
0.45

Splicing

Find out SpliceAI 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;