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GeneBe

rs116075389

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 0.0331 in 152,024 control chromosomes in the GnomAD database, including 145 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 0.033 ( 145 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.927
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 = 0.0758 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.0330
AC:
5019
AN:
151908
Hom.:
146
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0781
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0181
Gnomad ASJ
AF:
0.0199
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0278
Gnomad FIN
AF:
0.0115
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.0167
Gnomad OTH
AF:
0.0230
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0331
AC:
5029
AN:
152024
Hom.:
145
Cov.:
32
AF XY:
0.0325
AC XY:
2418
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.0780
Gnomad4 AMR
AF:
0.0181
Gnomad4 ASJ
AF:
0.0199
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0283
Gnomad4 FIN
AF:
0.0115
Gnomad4 NFE
AF:
0.0167
Gnomad4 OTH
AF:
0.0228
Alfa
AF:
0.0283
Hom.:
12
Bravo
AF:
0.0356
Asia WGS
AF:
0.0150
AC:
52
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
12
Dann
Benign
0.37

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: rs116075389; hg19: chr12-68957164; API