8-25152611-G-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 0.498 in 151,986 control chromosomes in the GnomAD database, including 19,195 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 0.50 ( 19195 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.173
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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 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:
0.498
AC:
75642
AN:
151866
Hom.:
19171
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.562
Gnomad AMI
AF:
0.443
Gnomad AMR
AF:
0.392
Gnomad ASJ
AF:
0.418
Gnomad EAS
AF:
0.338
Gnomad SAS
AF:
0.546
Gnomad FIN
AF:
0.467
Gnomad MID
AF:
0.459
Gnomad NFE
AF:
0.501
Gnomad OTH
AF:
0.519
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.498
AC:
75709
AN:
151986
Hom.:
19195
Cov.:
32
AF XY:
0.496
AC XY:
36886
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.562
Gnomad4 AMR
AF:
0.391
Gnomad4 ASJ
AF:
0.418
Gnomad4 EAS
AF:
0.339
Gnomad4 SAS
AF:
0.548
Gnomad4 FIN
AF:
0.467
Gnomad4 NFE
AF:
0.501
Gnomad4 OTH
AF:
0.518
Alfa
AF:
0.492
Hom.:
2208
Bravo
AF:
0.488
Asia WGS
AF:
0.439
AC:
1529
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
3.3
DANN
Benign
0.47

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: rs1405534; hg19: chr8-25010126; API