8-56909681-T-C

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 0.603 in 152,134 control chromosomes in the GnomAD database, including 28,196 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 0.60 ( 28196 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0790
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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 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:
0.603
AC:
91593
AN:
152016
Hom.:
28161
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.684
Gnomad AMI
AF:
0.353
Gnomad AMR
AF:
0.586
Gnomad ASJ
AF:
0.536
Gnomad EAS
AF:
0.795
Gnomad SAS
AF:
0.523
Gnomad FIN
AF:
0.655
Gnomad MID
AF:
0.554
Gnomad NFE
AF:
0.547
Gnomad OTH
AF:
0.587
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.603
AC:
91685
AN:
152134
Hom.:
28196
Cov.:
33
AF XY:
0.606
AC XY:
45089
AN XY:
74360
show subpopulations
Gnomad4 AFR
AF:
0.684
Gnomad4 AMR
AF:
0.587
Gnomad4 ASJ
AF:
0.536
Gnomad4 EAS
AF:
0.795
Gnomad4 SAS
AF:
0.525
Gnomad4 FIN
AF:
0.655
Gnomad4 NFE
AF:
0.547
Gnomad4 OTH
AF:
0.584
Alfa
AF:
0.588
Hom.:
4207
Bravo
AF:
0.607
Asia WGS
AF:
0.656
AC:
2278
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
6.3
DANN
Benign
0.65

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: rs985942; hg19: chr8-57822240; API