3-149437531-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 0.798 in 152,224 control chromosomes in the GnomAD database, including 48,604 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 0.80 ( 48604 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.453
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=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.828 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:
0.798
AC:
121379
AN:
152106
Hom.:
48554
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.815
Gnomad AMI
AF:
0.634
Gnomad AMR
AF:
0.840
Gnomad ASJ
AF:
0.680
Gnomad EAS
AF:
0.740
Gnomad SAS
AF:
0.835
Gnomad FIN
AF:
0.781
Gnomad MID
AF:
0.693
Gnomad NFE
AF:
0.791
Gnomad OTH
AF:
0.814
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.798
AC:
121487
AN:
152224
Hom.:
48604
Cov.:
33
AF XY:
0.797
AC XY:
59339
AN XY:
74428
show subpopulations
Gnomad4 AFR
AF:
0.815
Gnomad4 AMR
AF:
0.841
Gnomad4 ASJ
AF:
0.680
Gnomad4 EAS
AF:
0.740
Gnomad4 SAS
AF:
0.836
Gnomad4 FIN
AF:
0.781
Gnomad4 NFE
AF:
0.791
Gnomad4 OTH
AF:
0.816
Alfa
AF:
0.795
Hom.:
28886
Bravo
AF:
0.800
Asia WGS
AF:
0.817
AC:
2839
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
5.0
DANN
Benign
0.58

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: rs2043083; hg19: chr3-149155318; API