rs6018428

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 0.291 in 152,030 control chromosomes in the GnomAD database, including 8,964 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 0.29 ( 8964 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.409
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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.291
AC:
44176
AN:
151912
Hom.:
8941
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.578
Gnomad AMI
AF:
0.282
Gnomad AMR
AF:
0.241
Gnomad ASJ
AF:
0.175
Gnomad EAS
AF:
0.286
Gnomad SAS
AF:
0.171
Gnomad FIN
AF:
0.0994
Gnomad MID
AF:
0.253
Gnomad NFE
AF:
0.173
Gnomad OTH
AF:
0.269
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.291
AC:
44259
AN:
152030
Hom.:
8964
Cov.:
32
AF XY:
0.284
AC XY:
21117
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.578
Gnomad4 AMR
AF:
0.242
Gnomad4 ASJ
AF:
0.175
Gnomad4 EAS
AF:
0.285
Gnomad4 SAS
AF:
0.172
Gnomad4 FIN
AF:
0.0994
Gnomad4 NFE
AF:
0.173
Gnomad4 OTH
AF:
0.266
Alfa
AF:
0.200
Hom.:
2333
Bravo
AF:
0.315
Asia WGS
AF:
0.238
AC:
828
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
2.6
DANN
Benign
0.45

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: rs6018428; hg19: chr20-36051595; API