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GeneBe

rs7799039

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 0.366 in 152,070 control chromosomes in the GnomAD database, including 12,642 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 0.37 ( 12642 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.793
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 (EAS) allele frequency at 95% confidence interval = 0.724 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:
0.366
AC:
55641
AN:
151952
Hom.:
12638
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0976
Gnomad AMI
AF:
0.436
Gnomad AMR
AF:
0.432
Gnomad ASJ
AF:
0.418
Gnomad EAS
AF:
0.743
Gnomad SAS
AF:
0.525
Gnomad FIN
AF:
0.510
Gnomad MID
AF:
0.430
Gnomad NFE
AF:
0.449
Gnomad OTH
AF:
0.366
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.366
AC:
55647
AN:
152070
Hom.:
12642
Cov.:
33
AF XY:
0.377
AC XY:
28003
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.0973
Gnomad4 AMR
AF:
0.432
Gnomad4 ASJ
AF:
0.418
Gnomad4 EAS
AF:
0.744
Gnomad4 SAS
AF:
0.525
Gnomad4 FIN
AF:
0.510
Gnomad4 NFE
AF:
0.449
Gnomad4 OTH
AF:
0.370
Alfa
AF:
0.289
Hom.:
1142
Bravo
AF:
0.345
Asia WGS
AF:
0.621
AC:
2156
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
0.23
Dann
Benign
0.66

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: rs7799039; hg19: chr7-127878783; API