chr8-6939089-C-T

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 0.0777 in 152,164 control chromosomes in the GnomAD database, including 512 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 0.078 ( 512 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.709
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 = 0.0868 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:
0.0777
AC:
11820
AN:
152046
Hom.:
512
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0653
Gnomad AMI
AF:
0.104
Gnomad AMR
AF:
0.0834
Gnomad ASJ
AF:
0.168
Gnomad EAS
AF:
0.000578
Gnomad SAS
AF:
0.0695
Gnomad FIN
AF:
0.0527
Gnomad MID
AF:
0.149
Gnomad NFE
AF:
0.0886
Gnomad OTH
AF:
0.0939
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0777
AC:
11818
AN:
152164
Hom.:
512
Cov.:
32
AF XY:
0.0759
AC XY:
5648
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.0651
Gnomad4 AMR
AF:
0.0833
Gnomad4 ASJ
AF:
0.168
Gnomad4 EAS
AF:
0.000580
Gnomad4 SAS
AF:
0.0693
Gnomad4 FIN
AF:
0.0527
Gnomad4 NFE
AF:
0.0886
Gnomad4 OTH
AF:
0.0929
Alfa
AF:
0.0638
Hom.:
100
Bravo
AF:
0.0795
Asia WGS
AF:
0.0370
AC:
128
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
4.9
DANN
Benign
0.36

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: rs45482601; hg19: chr8-6796611; API