chr20-2803626-T-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 0.883 in 152,060 control chromosomes in the GnomAD database, including 59,416 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 0.88 ( 59416 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.15
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=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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:
0.883
AC:
134223
AN:
151942
Hom.:
59365
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.872
Gnomad AMI
AF:
0.805
Gnomad AMR
AF:
0.901
Gnomad ASJ
AF:
0.852
Gnomad EAS
AF:
0.998
Gnomad SAS
AF:
0.907
Gnomad FIN
AF:
0.876
Gnomad MID
AF:
0.860
Gnomad NFE
AF:
0.879
Gnomad OTH
AF:
0.890
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.883
AC:
134333
AN:
152060
Hom.:
59416
Cov.:
31
AF XY:
0.885
AC XY:
65748
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.873
Gnomad4 AMR
AF:
0.901
Gnomad4 ASJ
AF:
0.852
Gnomad4 EAS
AF:
0.998
Gnomad4 SAS
AF:
0.908
Gnomad4 FIN
AF:
0.876
Gnomad4 NFE
AF:
0.879
Gnomad4 OTH
AF:
0.891
Alfa
AF:
0.883
Hom.:
7369
Bravo
AF:
0.886
Asia WGS
AF:
0.951
AC:
3307
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
1.9
DANN
Benign
0.40

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: rs107130; hg19: chr20-2784272; API