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GeneBe

rs12779790

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 0.169 in 151424 control chromosomes in the gnomAD Genomes database, including 2231 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 0.17 ( 2231 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.198

Links

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.173 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:
0.169
AC:
25564
AN:
151424
Hom.:
2231
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.146
Gnomad AMI
AF:
0.105
Gnomad AMR
AF:
0.161
Gnomad ASJ
AF:
0.207
Gnomad EAS
AF:
0.183
Gnomad SAS
AF:
0.142
Gnomad FIN
AF:
0.214
Gnomad MID
AF:
0.136
Gnomad NFE
AF:
0.178
Gnomad OTH
AF:
0.166
Alfa
AF:
0.172
Hom.:
376
Bravo
AF:
0.164
Asia WGS
AF:
0.163
AC:
566
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
Cadd
Benign
2.5
Dann
Benign
0.25

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: rs12779790; hg19: chr10-12328010; API