rs8020281

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 0.284 in 151,226 control chromosomes in the GnomAD database, including 6,128 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 0.28 ( 6128 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.71
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=-1.06).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 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:
0.284
AC:
42896
AN:
151112
Hom.:
6128
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.325
Gnomad AMI
AF:
0.188
Gnomad AMR
AF:
0.266
Gnomad ASJ
AF:
0.169
Gnomad EAS
AF:
0.293
Gnomad SAS
AF:
0.284
Gnomad FIN
AF:
0.295
Gnomad MID
AF:
0.193
Gnomad NFE
AF:
0.269
Gnomad OTH
AF:
0.261
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.284
AC:
42930
AN:
151226
Hom.:
6128
Cov.:
32
AF XY:
0.285
AC XY:
21000
AN XY:
73782
show subpopulations
Gnomad4 AFR
AF:
0.324
Gnomad4 AMR
AF:
0.266
Gnomad4 ASJ
AF:
0.169
Gnomad4 EAS
AF:
0.293
Gnomad4 SAS
AF:
0.285
Gnomad4 FIN
AF:
0.295
Gnomad4 NFE
AF:
0.269
Gnomad4 OTH
AF:
0.263
Alfa
AF:
0.245
Hom.:
2102
Bravo
AF:
0.281
Asia WGS
AF:
0.334
AC:
1158
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.0030
DANN
Benign
0.43

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: rs8020281; hg19: chr14-95366426; API