rs720404

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 0.835 in 152,208 control chromosomes in the GnomAD database, including 53,817 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 0.84 ( 53817 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.721
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=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 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:
0.836
AC:
127088
AN:
152090
Hom.:
53791
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.681
Gnomad AMI
AF:
0.865
Gnomad AMR
AF:
0.926
Gnomad ASJ
AF:
0.935
Gnomad EAS
AF:
0.938
Gnomad SAS
AF:
0.885
Gnomad FIN
AF:
0.915
Gnomad MID
AF:
0.908
Gnomad NFE
AF:
0.879
Gnomad OTH
AF:
0.862
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.835
AC:
127156
AN:
152208
Hom.:
53817
Cov.:
33
AF XY:
0.840
AC XY:
62486
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.681
Gnomad4 AMR
AF:
0.926
Gnomad4 ASJ
AF:
0.935
Gnomad4 EAS
AF:
0.937
Gnomad4 SAS
AF:
0.886
Gnomad4 FIN
AF:
0.915
Gnomad4 NFE
AF:
0.879
Gnomad4 OTH
AF:
0.863
Alfa
AF:
0.869
Hom.:
28665
Bravo
AF:
0.830
Asia WGS
AF:
0.908
AC:
3156
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
4.1
DANN
Benign
0.49

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: rs720404; hg19: chr17-10882051; API