rs2054989

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 0.672 in 152,130 control chromosomes in the GnomAD database, including 35,242 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 0.67 ( 35242 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.74
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=-0.93).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.753 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:
0.672
AC:
102190
AN:
152012
Hom.:
35232
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.549
Gnomad AMI
AF:
0.679
Gnomad AMR
AF:
0.573
Gnomad ASJ
AF:
0.793
Gnomad EAS
AF:
0.556
Gnomad SAS
AF:
0.768
Gnomad FIN
AF:
0.707
Gnomad MID
AF:
0.848
Gnomad NFE
AF:
0.759
Gnomad OTH
AF:
0.684
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.672
AC:
102252
AN:
152130
Hom.:
35242
Cov.:
33
AF XY:
0.669
AC XY:
49738
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.550
Gnomad4 AMR
AF:
0.572
Gnomad4 ASJ
AF:
0.793
Gnomad4 EAS
AF:
0.556
Gnomad4 SAS
AF:
0.768
Gnomad4 FIN
AF:
0.707
Gnomad4 NFE
AF:
0.759
Gnomad4 OTH
AF:
0.683
Alfa
AF:
0.737
Hom.:
17610
Bravo
AF:
0.655
Asia WGS
AF:
0.663
AC:
2304
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.17
DANN
Benign
0.54

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: rs2054989; hg19: chr3-56530709; API