3-140821876-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 0.302 in 152,048 control chromosomes in the GnomAD database, including 7,010 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 0.30 ( 7010 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.215
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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 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:
0.302
AC:
45849
AN:
151930
Hom.:
7008
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.280
Gnomad AMI
AF:
0.269
Gnomad AMR
AF:
0.355
Gnomad ASJ
AF:
0.210
Gnomad EAS
AF:
0.443
Gnomad SAS
AF:
0.328
Gnomad FIN
AF:
0.310
Gnomad MID
AF:
0.225
Gnomad NFE
AF:
0.295
Gnomad OTH
AF:
0.290
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.302
AC:
45869
AN:
152048
Hom.:
7010
Cov.:
31
AF XY:
0.304
AC XY:
22620
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.280
Gnomad4 AMR
AF:
0.355
Gnomad4 ASJ
AF:
0.210
Gnomad4 EAS
AF:
0.442
Gnomad4 SAS
AF:
0.326
Gnomad4 FIN
AF:
0.310
Gnomad4 NFE
AF:
0.295
Gnomad4 OTH
AF:
0.296
Alfa
AF:
0.293
Hom.:
14340
Bravo
AF:
0.303
Asia WGS
AF:
0.362
AC:
1256
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
5.5
DANN
Benign
0.72

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: rs908821; hg19: chr3-140540718; API