GeneBe

1-152415662-C-T

Position:

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 0.87 in 152,190 control chromosomes in the GnomAD database, including 57,735 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 0.87 ( 57735 hom., cov: 31)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.609
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=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.152415662C>T intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FLG-AS1ENST00000411804.1 linkuse as main transcriptn.95-29182C>T intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.870
AC:
132240
AN:
152072
Hom.:
57678
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.929
Gnomad AMI
AF:
0.909
Gnomad AMR
AF:
0.882
Gnomad ASJ
AF:
0.853
Gnomad EAS
AF:
0.977
Gnomad SAS
AF:
0.948
Gnomad FIN
AF:
0.855
Gnomad MID
AF:
0.861
Gnomad NFE
AF:
0.819
Gnomad OTH
AF:
0.874
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.870
AC:
132356
AN:
152190
Hom.:
57735
Cov.:
31
AF XY:
0.874
AC XY:
64990
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.929
Gnomad4 AMR
AF:
0.882
Gnomad4 ASJ
AF:
0.853
Gnomad4 EAS
AF:
0.977
Gnomad4 SAS
AF:
0.948
Gnomad4 FIN
AF:
0.855
Gnomad4 NFE
AF:
0.819
Gnomad4 OTH
AF:
0.875
Alfa
AF:
0.841
Hom.:
32077
Bravo
AF:
0.872
Asia WGS
AF:
0.955
AC:
3323
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
4.8
DANN
Benign
0.19

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: rs4845763; hg19: chr1-152388138; API