Menu
GeneBe

rs121912961

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 0.0463 in 152,160 control chromosomes in the GnomAD database, including 210 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 0.046 ( 210 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.31
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.04).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0918 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:
0.0463
AC:
7036
AN:
152042
Hom.:
209
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0334
Gnomad AMI
AF:
0.0318
Gnomad AMR
AF:
0.0655
Gnomad ASJ
AF:
0.0623
Gnomad EAS
AF:
0.00907
Gnomad SAS
AF:
0.0988
Gnomad FIN
AF:
0.0327
Gnomad MID
AF:
0.0981
Gnomad NFE
AF:
0.0497
Gnomad OTH
AF:
0.0618
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0463
AC:
7039
AN:
152160
Hom.:
210
Cov.:
32
AF XY:
0.0459
AC XY:
3413
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.0334
Gnomad4 AMR
AF:
0.0655
Gnomad4 ASJ
AF:
0.0623
Gnomad4 EAS
AF:
0.00909
Gnomad4 SAS
AF:
0.0991
Gnomad4 FIN
AF:
0.0327
Gnomad4 NFE
AF:
0.0497
Gnomad4 OTH
AF:
0.0612
Alfa
AF:
0.0441
Hom.:
17
Bravo
AF:
0.0477
Asia WGS
AF:
0.0610
AC:
215
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
0.21
Dann
Benign
0.54

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: rs62312341; hg19: chr4-93071016; API