rs12084280

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 0.192 in 152,122 control chromosomes in the GnomAD database, including 4,183 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 0.19 ( 4183 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.421
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 (AFR) allele frequency at 95% confidence interval = 0.386 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:
0.192
AC:
29204
AN:
152004
Hom.:
4174
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.390
Gnomad AMI
AF:
0.0888
Gnomad AMR
AF:
0.160
Gnomad ASJ
AF:
0.0775
Gnomad EAS
AF:
0.349
Gnomad SAS
AF:
0.184
Gnomad FIN
AF:
0.117
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.0876
Gnomad OTH
AF:
0.170
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.192
AC:
29247
AN:
152122
Hom.:
4183
Cov.:
32
AF XY:
0.192
AC XY:
14305
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.391
Gnomad4 AMR
AF:
0.160
Gnomad4 ASJ
AF:
0.0775
Gnomad4 EAS
AF:
0.349
Gnomad4 SAS
AF:
0.182
Gnomad4 FIN
AF:
0.117
Gnomad4 NFE
AF:
0.0876
Gnomad4 OTH
AF:
0.169
Alfa
AF:
0.142
Hom.:
300
Bravo
AF:
0.203
Asia WGS
AF:
0.275
AC:
954
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
7.4
DANN
Benign
0.75

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: rs12084280; hg19: chr1-162023809; API