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GeneBe

rs12980275

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 0.355 in 151790 control chromosomes in the gnomAD Genomes database, including 10634 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 0.35 ( 10634 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.64

Links

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.07).
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 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:
0.355
AC:
53870
AN:
151790
Hom.:
10634
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.518
Gnomad AMI
AF:
0.330
Gnomad AMR
AF:
0.370
Gnomad ASJ
AF:
0.403
Gnomad EAS
AF:
0.0792
Gnomad SAS
AF:
0.216
Gnomad FIN
AF:
0.223
Gnomad MID
AF:
0.367
Gnomad NFE
AF:
0.302
Gnomad OTH
AF:
0.340
Alfa
AF:
0.316
Hom.:
18084
Bravo
AF:
0.374
Asia WGS
AF:
0.180
AC:
630
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
Cadd
Benign
0.67
Dann
Benign
0.17

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: rs12980275; hg19: chr19-39731783; API