3-23993497-G-C

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 0.609 in 151,184 control chromosomes in the GnomAD database, including 28,621 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 0.61 ( 28621 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01
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 (NFE) allele frequency at 95% confidence interval = 0.684 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:
0.609
AC:
92061
AN:
151068
Hom.:
28599
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.482
Gnomad AMI
AF:
0.485
Gnomad AMR
AF:
0.633
Gnomad ASJ
AF:
0.710
Gnomad EAS
AF:
0.482
Gnomad SAS
AF:
0.607
Gnomad FIN
AF:
0.594
Gnomad MID
AF:
0.732
Gnomad NFE
AF:
0.689
Gnomad OTH
AF:
0.628
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.609
AC:
92127
AN:
151184
Hom.:
28621
Cov.:
30
AF XY:
0.606
AC XY:
44765
AN XY:
73830
show subpopulations
Gnomad4 AFR
AF:
0.483
Gnomad4 AMR
AF:
0.633
Gnomad4 ASJ
AF:
0.710
Gnomad4 EAS
AF:
0.482
Gnomad4 SAS
AF:
0.607
Gnomad4 FIN
AF:
0.594
Gnomad4 NFE
AF:
0.689
Gnomad4 OTH
AF:
0.626
Alfa
AF:
0.639
Hom.:
3875
Bravo
AF:
0.607
Asia WGS
AF:
0.548
AC:
1907
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
0.49
DANN
Benign
0.48

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: rs6550826; hg19: chr3-24034988; API