rs6048205

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 0.09 in 151,904 control chromosomes in the GnomAD database, including 859 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 0.090 ( 859 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.517
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=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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:
0.0898
AC:
13635
AN:
151786
Hom.:
850
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.176
Gnomad AMI
AF:
0.127
Gnomad AMR
AF:
0.0513
Gnomad ASJ
AF:
0.103
Gnomad EAS
AF:
0.159
Gnomad SAS
AF:
0.0327
Gnomad FIN
AF:
0.0408
Gnomad MID
AF:
0.0728
Gnomad NFE
AF:
0.0515
Gnomad OTH
AF:
0.0856
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0900
AC:
13667
AN:
151904
Hom.:
859
Cov.:
31
AF XY:
0.0880
AC XY:
6531
AN XY:
74234
show subpopulations
Gnomad4 AFR
AF:
0.177
Gnomad4 AMR
AF:
0.0511
Gnomad4 ASJ
AF:
0.103
Gnomad4 EAS
AF:
0.159
Gnomad4 SAS
AF:
0.0325
Gnomad4 FIN
AF:
0.0408
Gnomad4 NFE
AF:
0.0515
Gnomad4 OTH
AF:
0.0871
Alfa
AF:
0.0581
Hom.:
403
Bravo
AF:
0.0959
Asia WGS
AF:
0.111
AC:
386
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
5.9
DANN
Benign
0.27

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: rs6048205; hg19: chr20-22559601; API