rs1476202

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 0.805 in 152,222 control chromosomes in the GnomAD database, including 49,480 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 0.81 ( 49480 hom., cov: 34)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.06
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=-1.0).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.841 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:
0.805
AC:
122498
AN:
152104
Hom.:
49430
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.823
Gnomad AMI
AF:
0.814
Gnomad AMR
AF:
0.853
Gnomad ASJ
AF:
0.842
Gnomad EAS
AF:
0.786
Gnomad SAS
AF:
0.698
Gnomad FIN
AF:
0.836
Gnomad MID
AF:
0.854
Gnomad NFE
AF:
0.786
Gnomad OTH
AF:
0.802
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.805
AC:
122601
AN:
152222
Hom.:
49480
Cov.:
34
AF XY:
0.807
AC XY:
60058
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.823
Gnomad4 AMR
AF:
0.854
Gnomad4 ASJ
AF:
0.842
Gnomad4 EAS
AF:
0.785
Gnomad4 SAS
AF:
0.699
Gnomad4 FIN
AF:
0.836
Gnomad4 NFE
AF:
0.786
Gnomad4 OTH
AF:
0.795
Alfa
AF:
0.785
Hom.:
18725
Bravo
AF:
0.811
Asia WGS
AF:
0.737
AC:
2563
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
0.15
DANN
Benign
0.40

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: rs1476202; hg19: chr11-123816214; API