rs1369976

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 0.927 in 152,020 control chromosomes in the GnomAD database, including 65,333 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 0.93 ( 65333 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.187
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=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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:
0.927
AC:
140784
AN:
151902
Hom.:
65298
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.925
Gnomad AMI
AF:
0.964
Gnomad AMR
AF:
0.934
Gnomad ASJ
AF:
0.912
Gnomad EAS
AF:
0.998
Gnomad SAS
AF:
0.868
Gnomad FIN
AF:
0.971
Gnomad MID
AF:
0.858
Gnomad NFE
AF:
0.918
Gnomad OTH
AF:
0.927
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.927
AC:
140874
AN:
152020
Hom.:
65333
Cov.:
32
AF XY:
0.928
AC XY:
68965
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.925
Gnomad4 AMR
AF:
0.934
Gnomad4 ASJ
AF:
0.912
Gnomad4 EAS
AF:
0.998
Gnomad4 SAS
AF:
0.868
Gnomad4 FIN
AF:
0.971
Gnomad4 NFE
AF:
0.918
Gnomad4 OTH
AF:
0.925
Alfa
AF:
0.907
Hom.:
61946
Bravo
AF:
0.926
Asia WGS
AF:
0.919
AC:
3196
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
4.9
DANN
Benign
0.73

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: rs1369976; hg19: chr4-96807307; API