14-99683121-A-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 0.679 in 152,084 control chromosomes in the GnomAD database, including 36,267 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 0.68 ( 36267 hom., cov: 33)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.74
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.99683121A>G intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.679
AC:
103158
AN:
151968
Hom.:
36266
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.490
Gnomad AMI
AF:
0.808
Gnomad AMR
AF:
0.688
Gnomad ASJ
AF:
0.761
Gnomad EAS
AF:
0.601
Gnomad SAS
AF:
0.842
Gnomad FIN
AF:
0.748
Gnomad MID
AF:
0.763
Gnomad NFE
AF:
0.769
Gnomad OTH
AF:
0.681
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.679
AC:
103199
AN:
152084
Hom.:
36267
Cov.:
33
AF XY:
0.681
AC XY:
50649
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.490
Gnomad4 AMR
AF:
0.688
Gnomad4 ASJ
AF:
0.761
Gnomad4 EAS
AF:
0.601
Gnomad4 SAS
AF:
0.841
Gnomad4 FIN
AF:
0.748
Gnomad4 NFE
AF:
0.769
Gnomad4 OTH
AF:
0.680
Alfa
AF:
0.680
Hom.:
5830
Bravo
AF:
0.664
Asia WGS
AF:
0.711
AC:
2477
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
2.8
DANN
Benign
0.42

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: rs3783320; hg19: chr14-100149458; API