chr3-46324778-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 0.736 in 152,176 control chromosomes in the GnomAD database, including 41,618 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 0.74 ( 41618 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.196
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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 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:
0.736
AC:
111869
AN:
152058
Hom.:
41558
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.850
Gnomad AMI
AF:
0.666
Gnomad AMR
AF:
0.675
Gnomad ASJ
AF:
0.735
Gnomad EAS
AF:
0.696
Gnomad SAS
AF:
0.656
Gnomad FIN
AF:
0.711
Gnomad MID
AF:
0.627
Gnomad NFE
AF:
0.694
Gnomad OTH
AF:
0.713
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.736
AC:
111981
AN:
152176
Hom.:
41618
Cov.:
32
AF XY:
0.732
AC XY:
54457
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.850
Gnomad4 AMR
AF:
0.675
Gnomad4 ASJ
AF:
0.735
Gnomad4 EAS
AF:
0.697
Gnomad4 SAS
AF:
0.657
Gnomad4 FIN
AF:
0.711
Gnomad4 NFE
AF:
0.694
Gnomad4 OTH
AF:
0.716
Alfa
AF:
0.729
Hom.:
9435
Bravo
AF:
0.743
Asia WGS
AF:
0.712
AC:
2477
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.88
DANN
Benign
0.62

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: rs2157057; hg19: chr3-46366269; API