rs10796849

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 0.692 in 152,026 control chromosomes in the GnomAD database, including 39,470 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 0.69 ( 39470 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.437
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.849 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:
0.692
AC:
105109
AN:
151908
Hom.:
39474
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.403
Gnomad AMI
AF:
0.954
Gnomad AMR
AF:
0.624
Gnomad ASJ
AF:
0.821
Gnomad EAS
AF:
0.571
Gnomad SAS
AF:
0.680
Gnomad FIN
AF:
0.862
Gnomad MID
AF:
0.848
Gnomad NFE
AF:
0.855
Gnomad OTH
AF:
0.725
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.692
AC:
105126
AN:
152026
Hom.:
39470
Cov.:
32
AF XY:
0.691
AC XY:
51305
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.402
Gnomad4 AMR
AF:
0.624
Gnomad4 ASJ
AF:
0.821
Gnomad4 EAS
AF:
0.570
Gnomad4 SAS
AF:
0.680
Gnomad4 FIN
AF:
0.862
Gnomad4 NFE
AF:
0.854
Gnomad4 OTH
AF:
0.724
Alfa
AF:
0.763
Hom.:
5809
Bravo
AF:
0.662
Asia WGS
AF:
0.640
AC:
2226
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
1.2
DANN
Benign
0.31

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: rs10796849; hg19: chr11-69602412; API