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GeneBe

rs662799

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 0.899 in 152,224 control chromosomes in the GnomAD database, including 61,676 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 0.90 ( 61676 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00200
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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.929 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:
0.899
AC:
136711
AN:
152106
Hom.:
61657
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.880
Gnomad AMI
AF:
0.935
Gnomad AMR
AF:
0.867
Gnomad ASJ
AF:
0.912
Gnomad EAS
AF:
0.699
Gnomad SAS
AF:
0.811
Gnomad FIN
AF:
0.921
Gnomad MID
AF:
0.877
Gnomad NFE
AF:
0.935
Gnomad OTH
AF:
0.890
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.899
AC:
136785
AN:
152224
Hom.:
61676
Cov.:
32
AF XY:
0.895
AC XY:
66601
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.880
Gnomad4 AMR
AF:
0.867
Gnomad4 ASJ
AF:
0.912
Gnomad4 EAS
AF:
0.698
Gnomad4 SAS
AF:
0.811
Gnomad4 FIN
AF:
0.921
Gnomad4 NFE
AF:
0.935
Gnomad4 OTH
AF:
0.885
Alfa
AF:
0.913
Hom.:
23370
Bravo
AF:
0.894
Asia WGS
AF:
0.767
AC:
2668
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
0.93
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: rs662799; hg19: chr11-116663707; API