10-121598798-A-G

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 0.868 in 152,226 control chromosomes in the GnomAD database, including 57,853 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 0.87 ( 57853 hom., cov: 34)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.217
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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 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:
0.868
AC:
132061
AN:
152110
Hom.:
57817
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.740
Gnomad AMI
AF:
0.840
Gnomad AMR
AF:
0.912
Gnomad ASJ
AF:
0.930
Gnomad EAS
AF:
0.972
Gnomad SAS
AF:
0.960
Gnomad FIN
AF:
0.934
Gnomad MID
AF:
0.873
Gnomad NFE
AF:
0.908
Gnomad OTH
AF:
0.876
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.868
AC:
132155
AN:
152226
Hom.:
57853
Cov.:
34
AF XY:
0.872
AC XY:
64923
AN XY:
74434
show subpopulations
Gnomad4 AFR
AF:
0.740
Gnomad4 AMR
AF:
0.913
Gnomad4 ASJ
AF:
0.930
Gnomad4 EAS
AF:
0.972
Gnomad4 SAS
AF:
0.960
Gnomad4 FIN
AF:
0.934
Gnomad4 NFE
AF:
0.908
Gnomad4 OTH
AF:
0.877
Alfa
AF:
0.900
Hom.:
55147
Bravo
AF:
0.861
Asia WGS
AF:
0.953
AC:
3312
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
5.8
DANN
Benign
0.59

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: rs1219639; hg19: chr10-123358312; API