8-125465736-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 0.594 in 152,044 control chromosomes in the GnomAD database, including 27,980 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 0.59 ( 27980 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0120
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 (AFR) allele frequency at 95% confidence interval = 0.783 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:
0.594
AC:
90203
AN:
151926
Hom.:
27929
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.790
Gnomad AMI
AF:
0.661
Gnomad AMR
AF:
0.501
Gnomad ASJ
AF:
0.425
Gnomad EAS
AF:
0.548
Gnomad SAS
AF:
0.469
Gnomad FIN
AF:
0.552
Gnomad MID
AF:
0.443
Gnomad NFE
AF:
0.524
Gnomad OTH
AF:
0.559
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.594
AC:
90307
AN:
152044
Hom.:
27980
Cov.:
32
AF XY:
0.589
AC XY:
43763
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.790
Gnomad4 AMR
AF:
0.501
Gnomad4 ASJ
AF:
0.425
Gnomad4 EAS
AF:
0.549
Gnomad4 SAS
AF:
0.467
Gnomad4 FIN
AF:
0.552
Gnomad4 NFE
AF:
0.524
Gnomad4 OTH
AF:
0.565
Alfa
AF:
0.432
Hom.:
1152
Bravo
AF:
0.598
Asia WGS
AF:
0.551
AC:
1920
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
8.2
DANN
Benign
0.72

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: rs2001945; hg19: chr8-126477978; API