rs2829946

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 0.15 in 152,160 control chromosomes in the GnomAD database, including 1,843 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 0.15 ( 1843 hom., cov: 32)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.117
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=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.25844046C>T intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.150
AC:
22860
AN:
152042
Hom.:
1837
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.161
Gnomad AMI
AF:
0.281
Gnomad AMR
AF:
0.121
Gnomad ASJ
AF:
0.0910
Gnomad EAS
AF:
0.00309
Gnomad SAS
AF:
0.0937
Gnomad FIN
AF:
0.176
Gnomad MID
AF:
0.136
Gnomad NFE
AF:
0.163
Gnomad OTH
AF:
0.136
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.150
AC:
22884
AN:
152160
Hom.:
1843
Cov.:
32
AF XY:
0.149
AC XY:
11094
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.161
Gnomad4 AMR
AF:
0.121
Gnomad4 ASJ
AF:
0.0910
Gnomad4 EAS
AF:
0.00329
Gnomad4 SAS
AF:
0.0937
Gnomad4 FIN
AF:
0.176
Gnomad4 NFE
AF:
0.164
Gnomad4 OTH
AF:
0.135
Alfa
AF:
0.155
Hom.:
2956
Bravo
AF:
0.147
Asia WGS
AF:
0.0600
AC:
214
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
4.8
DANN
Benign
0.67

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: rs2829946; hg19: chr21-27216357; API