GeneBe

2-48815260-A-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 0.226 in 152,120 control chromosomes in the GnomAD database, including 5,021 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 0.23 ( 5021 hom., cov: 32)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.22
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.48815260A>T intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000282890ENST00000634588.1 linkuse as main transcriptn.302+5619A>T intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.226
AC:
34373
AN:
152002
Hom.:
5030
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0580
Gnomad AMI
AF:
0.146
Gnomad AMR
AF:
0.205
Gnomad ASJ
AF:
0.325
Gnomad EAS
AF:
0.575
Gnomad SAS
AF:
0.318
Gnomad FIN
AF:
0.321
Gnomad MID
AF:
0.234
Gnomad NFE
AF:
0.281
Gnomad OTH
AF:
0.231
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.226
AC:
34358
AN:
152120
Hom.:
5021
Cov.:
32
AF XY:
0.232
AC XY:
17238
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.0579
Gnomad4 AMR
AF:
0.204
Gnomad4 ASJ
AF:
0.325
Gnomad4 EAS
AF:
0.574
Gnomad4 SAS
AF:
0.317
Gnomad4 FIN
AF:
0.321
Gnomad4 NFE
AF:
0.281
Gnomad4 OTH
AF:
0.230
Alfa
AF:
0.104
Hom.:
183
Bravo
AF:
0.208
Asia WGS
AF:
0.385
AC:
1337
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.020
DANN
Benign
0.60

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: rs9636432; hg19: chr2-49042399; API