chr7-108457047-C-G

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 0.0942 in 151,734 control chromosomes in the GnomAD database, including 714 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 0.094 ( 714 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.947
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=-0.83).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 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:
0.0942
AC:
14289
AN:
151618
Hom.:
714
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0745
Gnomad AMI
AF:
0.0417
Gnomad AMR
AF:
0.0878
Gnomad ASJ
AF:
0.0706
Gnomad EAS
AF:
0.0585
Gnomad SAS
AF:
0.0889
Gnomad FIN
AF:
0.151
Gnomad MID
AF:
0.0981
Gnomad NFE
AF:
0.104
Gnomad OTH
AF:
0.0975
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0942
AC:
14293
AN:
151734
Hom.:
714
Cov.:
31
AF XY:
0.0960
AC XY:
7112
AN XY:
74108
show subpopulations
Gnomad4 AFR
AF:
0.0744
Gnomad4 AMR
AF:
0.0876
Gnomad4 ASJ
AF:
0.0706
Gnomad4 EAS
AF:
0.0590
Gnomad4 SAS
AF:
0.0887
Gnomad4 FIN
AF:
0.151
Gnomad4 NFE
AF:
0.104
Gnomad4 OTH
AF:
0.0966
Alfa
AF:
0.0950
Hom.:
87
Bravo
AF:
0.0875
Asia WGS
AF:
0.0820
AC:
285
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.2
DANN
Benign
0.61

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: rs3763463; hg19: chr7-108097491; API