8-114759725-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 0.107 in 152,238 control chromosomes in the GnomAD database, including 1,475 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 0.11 ( 1475 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.157
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 = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.107
AC:
16335
AN:
152120
Hom.:
1476
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.253
Gnomad AMI
AF:
0.0406
Gnomad AMR
AF:
0.0829
Gnomad ASJ
AF:
0.0458
Gnomad EAS
AF:
0.0922
Gnomad SAS
AF:
0.0714
Gnomad FIN
AF:
0.0454
Gnomad MID
AF:
0.0601
Gnomad NFE
AF:
0.0428
Gnomad OTH
AF:
0.0817
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.107
AC:
16346
AN:
152238
Hom.:
1475
Cov.:
32
AF XY:
0.108
AC XY:
8037
AN XY:
74430
show subpopulations
Gnomad4 AFR
AF:
0.253
Gnomad4 AMR
AF:
0.0827
Gnomad4 ASJ
AF:
0.0458
Gnomad4 EAS
AF:
0.0916
Gnomad4 SAS
AF:
0.0712
Gnomad4 FIN
AF:
0.0454
Gnomad4 NFE
AF:
0.0428
Gnomad4 OTH
AF:
0.0808
Alfa
AF:
0.0802
Hom.:
146
Bravo
AF:
0.117
Asia WGS
AF:
0.0860
AC:
298
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.63
DANN
Benign
0.48

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: rs2045155; hg19: chr8-115771954; API