rs7789066

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 0.0821 in 152,110 control chromosomes in the GnomAD database, including 573 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 0.082 ( 573 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.324
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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 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:
0.0820
AC:
12457
AN:
151992
Hom.:
569
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.124
Gnomad AMI
AF:
0.0373
Gnomad AMR
AF:
0.0724
Gnomad ASJ
AF:
0.126
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.0229
Gnomad FIN
AF:
0.0645
Gnomad MID
AF:
0.142
Gnomad NFE
AF:
0.0693
Gnomad OTH
AF:
0.0948
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0821
AC:
12491
AN:
152110
Hom.:
573
Cov.:
33
AF XY:
0.0807
AC XY:
6001
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.125
Gnomad4 AMR
AF:
0.0722
Gnomad4 ASJ
AF:
0.126
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.0236
Gnomad4 FIN
AF:
0.0645
Gnomad4 NFE
AF:
0.0693
Gnomad4 OTH
AF:
0.0943
Alfa
AF:
0.0700
Hom.:
865
Bravo
AF:
0.0842

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
5.3
DANN
Benign
0.78

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: rs7789066; hg19: chr7-105927752; API