rs2093395

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 0.29 in 152,076 control chromosomes in the GnomAD database, including 6,528 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 ( 6528 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.336
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=-0.93).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.351 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:
0.290
AC:
43995
AN:
151958
Hom.:
6525
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.226
Gnomad AMI
AF:
0.295
Gnomad AMR
AF:
0.359
Gnomad ASJ
AF:
0.301
Gnomad EAS
AF:
0.345
Gnomad SAS
AF:
0.337
Gnomad FIN
AF:
0.311
Gnomad MID
AF:
0.272
Gnomad NFE
AF:
0.301
Gnomad OTH
AF:
0.292
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.290
AC:
44036
AN:
152076
Hom.:
6528
Cov.:
32
AF XY:
0.293
AC XY:
21804
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.226
Gnomad4 AMR
AF:
0.359
Gnomad4 ASJ
AF:
0.301
Gnomad4 EAS
AF:
0.344
Gnomad4 SAS
AF:
0.338
Gnomad4 FIN
AF:
0.311
Gnomad4 NFE
AF:
0.301
Gnomad4 OTH
AF:
0.289
Alfa
AF:
0.309
Hom.:
922
Bravo
AF:
0.290
Asia WGS
AF:
0.367
AC:
1273
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
2.0
DANN
Benign
0.55

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: rs2093395; hg19: chr6-41155026; API