rs2206285

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 0.0592 in 152,266 control chromosomes in the GnomAD database, including 325 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 0.059 ( 325 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.08
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=-1.03).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0858 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:
0.0593
AC:
9019
AN:
152148
Hom.:
325
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0883
Gnomad AMI
AF:
0.0110
Gnomad AMR
AF:
0.0548
Gnomad ASJ
AF:
0.0703
Gnomad EAS
AF:
0.000577
Gnomad SAS
AF:
0.00559
Gnomad FIN
AF:
0.0333
Gnomad MID
AF:
0.0728
Gnomad NFE
AF:
0.0551
Gnomad OTH
AF:
0.0564
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0592
AC:
9021
AN:
152266
Hom.:
325
Cov.:
33
AF XY:
0.0570
AC XY:
4247
AN XY:
74476
show subpopulations
Gnomad4 AFR
AF:
0.0882
Gnomad4 AMR
AF:
0.0546
Gnomad4 ASJ
AF:
0.0703
Gnomad4 EAS
AF:
0.000578
Gnomad4 SAS
AF:
0.00559
Gnomad4 FIN
AF:
0.0333
Gnomad4 NFE
AF:
0.0551
Gnomad4 OTH
AF:
0.0558
Alfa
AF:
0.0588
Hom.:
36
Bravo
AF:
0.0615
Asia WGS
AF:
0.0100
AC:
35
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.34
DANN
Benign
0.65

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: rs2206285; hg19: chr6-170904958; API