chr20-6780865-C-T

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 0.703 in 152,048 control chromosomes in the GnomAD database, including 38,735 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 0.70 ( 38735 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.206
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=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 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:
0.703
AC:
106759
AN:
151928
Hom.:
38690
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.886
Gnomad AMI
AF:
0.628
Gnomad AMR
AF:
0.683
Gnomad ASJ
AF:
0.821
Gnomad EAS
AF:
0.672
Gnomad SAS
AF:
0.569
Gnomad FIN
AF:
0.574
Gnomad MID
AF:
0.756
Gnomad NFE
AF:
0.622
Gnomad OTH
AF:
0.715
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.703
AC:
106849
AN:
152048
Hom.:
38735
Cov.:
32
AF XY:
0.696
AC XY:
51754
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.886
Gnomad4 AMR
AF:
0.683
Gnomad4 ASJ
AF:
0.821
Gnomad4 EAS
AF:
0.672
Gnomad4 SAS
AF:
0.568
Gnomad4 FIN
AF:
0.574
Gnomad4 NFE
AF:
0.622
Gnomad4 OTH
AF:
0.708
Alfa
AF:
0.698
Hom.:
6422
Bravo
AF:
0.723
Asia WGS
AF:
0.609
AC:
2114
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
9.4
DANN
Benign
0.66

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: rs6054512; hg19: chr20-6761512; API