rs3021529

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 0.126 in 152,132 control chromosomes in the GnomAD database, including 1,301 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 0.13 ( 1301 hom., cov: 32)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.206
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=-0.79).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.63151900G>A intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000279444ENST00000624438.1 linkuse as main transcriptn.29-581G>A intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.126
AC:
19215
AN:
152014
Hom.:
1299
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.112
Gnomad AMI
AF:
0.255
Gnomad AMR
AF:
0.110
Gnomad ASJ
AF:
0.155
Gnomad EAS
AF:
0.0380
Gnomad SAS
AF:
0.159
Gnomad FIN
AF:
0.0944
Gnomad MID
AF:
0.120
Gnomad NFE
AF:
0.145
Gnomad OTH
AF:
0.122
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.126
AC:
19235
AN:
152132
Hom.:
1301
Cov.:
32
AF XY:
0.125
AC XY:
9274
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.112
Gnomad4 AMR
AF:
0.110
Gnomad4 ASJ
AF:
0.155
Gnomad4 EAS
AF:
0.0383
Gnomad4 SAS
AF:
0.160
Gnomad4 FIN
AF:
0.0944
Gnomad4 NFE
AF:
0.145
Gnomad4 OTH
AF:
0.121
Alfa
AF:
0.140
Hom.:
2008
Bravo
AF:
0.123
Asia WGS
AF:
0.0980
AC:
338
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
9.1
DANN
Benign
0.93

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: rs3021529; hg19: chr12-63545680; API