GeneBe

18-2292492-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 0.551 in 151,294 control chromosomes in the GnomAD database, including 23,065 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 0.55 ( 23065 hom., cov: 30)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.85
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=-1.03).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.2292492C>T intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000263745ENST00000639316.2 linkuse as main transcriptn.354+42578G>A intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.551
AC:
83272
AN:
151178
Hom.:
23028
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.574
Gnomad AMI
AF:
0.481
Gnomad AMR
AF:
0.552
Gnomad ASJ
AF:
0.570
Gnomad EAS
AF:
0.698
Gnomad SAS
AF:
0.551
Gnomad FIN
AF:
0.443
Gnomad MID
AF:
0.490
Gnomad NFE
AF:
0.542
Gnomad OTH
AF:
0.567
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.551
AC:
83363
AN:
151294
Hom.:
23065
Cov.:
30
AF XY:
0.546
AC XY:
40386
AN XY:
73906
show subpopulations
Gnomad4 AFR
AF:
0.575
Gnomad4 AMR
AF:
0.552
Gnomad4 ASJ
AF:
0.570
Gnomad4 EAS
AF:
0.699
Gnomad4 SAS
AF:
0.551
Gnomad4 FIN
AF:
0.443
Gnomad4 NFE
AF:
0.542
Gnomad4 OTH
AF:
0.565
Alfa
AF:
0.547
Hom.:
45967
Bravo
AF:
0.561
Asia WGS
AF:
0.623
AC:
2163
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.81
DANN
Benign
0.36

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: rs627202; hg19: chr18-2292491; API