8-90123850-T-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 0.545 in 151,974 control chromosomes in the GnomAD database, including 24,199 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 0.54 ( 24199 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.90
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=-0.8).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.668 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:
0.545
AC:
82774
AN:
151856
Hom.:
24205
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.353
Gnomad AMI
AF:
0.732
Gnomad AMR
AF:
0.490
Gnomad ASJ
AF:
0.702
Gnomad EAS
AF:
0.307
Gnomad SAS
AF:
0.533
Gnomad FIN
AF:
0.595
Gnomad MID
AF:
0.687
Gnomad NFE
AF:
0.674
Gnomad OTH
AF:
0.571
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.545
AC:
82785
AN:
151974
Hom.:
24199
Cov.:
32
AF XY:
0.538
AC XY:
39988
AN XY:
74286
show subpopulations
Gnomad4 AFR
AF:
0.353
Gnomad4 AMR
AF:
0.490
Gnomad4 ASJ
AF:
0.702
Gnomad4 EAS
AF:
0.309
Gnomad4 SAS
AF:
0.531
Gnomad4 FIN
AF:
0.595
Gnomad4 NFE
AF:
0.674
Gnomad4 OTH
AF:
0.567
Alfa
AF:
0.650
Hom.:
39786
Bravo
AF:
0.528
Asia WGS
AF:
0.396
AC:
1377
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
14
DANN
Benign
0.76

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: rs2205108; hg19: chr8-91136078; API