rs8099014

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 0.653 in 152,094 control chromosomes in the GnomAD database, including 33,697 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 0.65 ( 33697 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.16
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=-0.81).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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:
0.653
AC:
99242
AN:
151976
Hom.:
33691
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.446
Gnomad AMI
AF:
0.804
Gnomad AMR
AF:
0.730
Gnomad ASJ
AF:
0.726
Gnomad EAS
AF:
0.754
Gnomad SAS
AF:
0.625
Gnomad FIN
AF:
0.724
Gnomad MID
AF:
0.631
Gnomad NFE
AF:
0.738
Gnomad OTH
AF:
0.672
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.653
AC:
99271
AN:
152094
Hom.:
33697
Cov.:
33
AF XY:
0.652
AC XY:
48526
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.446
Gnomad4 AMR
AF:
0.730
Gnomad4 ASJ
AF:
0.726
Gnomad4 EAS
AF:
0.753
Gnomad4 SAS
AF:
0.626
Gnomad4 FIN
AF:
0.724
Gnomad4 NFE
AF:
0.739
Gnomad4 OTH
AF:
0.671
Alfa
AF:
0.724
Hom.:
87823
Bravo
AF:
0.647
Asia WGS
AF:
0.674
AC:
2346
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
11
DANN
Benign
0.71

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: rs8099014; hg19: chr18-56109859; API