rs6097169

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 0.139 in 152,140 control chromosomes in the GnomAD database, including 1,988 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 0.14 ( 1988 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.01
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=-0.79).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 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:
0.139
AC:
21055
AN:
152022
Hom.:
1974
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.161
Gnomad AMI
AF:
0.0670
Gnomad AMR
AF:
0.133
Gnomad ASJ
AF:
0.121
Gnomad EAS
AF:
0.528
Gnomad SAS
AF:
0.234
Gnomad FIN
AF:
0.101
Gnomad MID
AF:
0.0949
Gnomad NFE
AF:
0.0984
Gnomad OTH
AF:
0.118
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.139
AC:
21104
AN:
152140
Hom.:
1988
Cov.:
33
AF XY:
0.144
AC XY:
10681
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.161
Gnomad4 AMR
AF:
0.133
Gnomad4 ASJ
AF:
0.121
Gnomad4 EAS
AF:
0.530
Gnomad4 SAS
AF:
0.234
Gnomad4 FIN
AF:
0.101
Gnomad4 NFE
AF:
0.0984
Gnomad4 OTH
AF:
0.125
Alfa
AF:
0.116
Hom.:
528
Bravo
AF:
0.141
Asia WGS
AF:
0.381
AC:
1320
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
16
DANN
Benign
0.68

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: rs6097169; hg19: chr20-51557161; API