chr3-12681371-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 0.493 in 151,944 control chromosomes in the GnomAD database, including 19,289 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 0.49 ( 19289 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.72
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=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.493
AC:
74870
AN:
151826
Hom.:
19288
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.389
Gnomad AMI
AF:
0.301
Gnomad AMR
AF:
0.470
Gnomad ASJ
AF:
0.551
Gnomad EAS
AF:
0.892
Gnomad SAS
AF:
0.748
Gnomad FIN
AF:
0.488
Gnomad MID
AF:
0.598
Gnomad NFE
AF:
0.513
Gnomad OTH
AF:
0.498
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.493
AC:
74909
AN:
151944
Hom.:
19289
Cov.:
32
AF XY:
0.497
AC XY:
36925
AN XY:
74238
show subpopulations
Gnomad4 AFR
AF:
0.389
Gnomad4 AMR
AF:
0.471
Gnomad4 ASJ
AF:
0.551
Gnomad4 EAS
AF:
0.892
Gnomad4 SAS
AF:
0.748
Gnomad4 FIN
AF:
0.488
Gnomad4 NFE
AF:
0.513
Gnomad4 OTH
AF:
0.495
Alfa
AF:
0.518
Hom.:
40841
Bravo
AF:
0.481
Asia WGS
AF:
0.722
AC:
2509
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
5.7
DANN
Benign
0.64

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: rs6442323; hg19: chr3-12722870; API