rs1243168

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 0.849 in 152,252 control chromosomes in the GnomAD database, including 55,329 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 0.85 ( 55329 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.270
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 (AFR) allele frequency at 95% confidence interval = 0.949 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:
0.849
AC:
129137
AN:
152134
Hom.:
55266
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.956
Gnomad AMI
AF:
0.800
Gnomad AMR
AF:
0.870
Gnomad ASJ
AF:
0.825
Gnomad EAS
AF:
0.944
Gnomad SAS
AF:
0.894
Gnomad FIN
AF:
0.791
Gnomad MID
AF:
0.866
Gnomad NFE
AF:
0.779
Gnomad OTH
AF:
0.858
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.849
AC:
129259
AN:
152252
Hom.:
55329
Cov.:
33
AF XY:
0.853
AC XY:
63495
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.956
Gnomad4 AMR
AF:
0.870
Gnomad4 ASJ
AF:
0.825
Gnomad4 EAS
AF:
0.944
Gnomad4 SAS
AF:
0.894
Gnomad4 FIN
AF:
0.791
Gnomad4 NFE
AF:
0.779
Gnomad4 OTH
AF:
0.858
Alfa
AF:
0.801
Hom.:
22326
Bravo
AF:
0.860
Asia WGS
AF:
0.907
AC:
3152
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
2.6
DANN
Benign
0.58

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: rs1243168; hg19: chr14-94841366; API