chr2-143898268-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 0.77 in 152,144 control chromosomes in the GnomAD database, including 45,299 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 0.77 ( 45299 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.675
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 (EAS) allele frequency at 95% confidence interval = 0.944 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:
0.770
AC:
117054
AN:
152026
Hom.:
45272
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.763
Gnomad AMI
AF:
0.908
Gnomad AMR
AF:
0.803
Gnomad ASJ
AF:
0.650
Gnomad EAS
AF:
0.966
Gnomad SAS
AF:
0.899
Gnomad FIN
AF:
0.748
Gnomad MID
AF:
0.699
Gnomad NFE
AF:
0.751
Gnomad OTH
AF:
0.747
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.770
AC:
117131
AN:
152144
Hom.:
45299
Cov.:
33
AF XY:
0.772
AC XY:
57419
AN XY:
74398
show subpopulations
Gnomad4 AFR
AF:
0.763
Gnomad4 AMR
AF:
0.803
Gnomad4 ASJ
AF:
0.650
Gnomad4 EAS
AF:
0.966
Gnomad4 SAS
AF:
0.899
Gnomad4 FIN
AF:
0.748
Gnomad4 NFE
AF:
0.751
Gnomad4 OTH
AF:
0.750
Alfa
AF:
0.756
Hom.:
58358
Bravo
AF:
0.773
Asia WGS
AF:
0.904
AC:
3144
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
5.6
DANN
Benign
0.79

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: rs787151; hg19: chr2-144655836; API