rs32934

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 0.0722 in 152,306 control chromosomes in the GnomAD database, including 729 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 0.072 ( 729 hom., cov: 33)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.280
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=-0.72).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.76714881C>T intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000225407ENST00000507514.1 linkuse as main transcriptn.39+1296G>A intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0721
AC:
10980
AN:
152188
Hom.:
727
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0530
Gnomad AMI
AF:
0.0471
Gnomad AMR
AF:
0.0688
Gnomad ASJ
AF:
0.0377
Gnomad EAS
AF:
0.406
Gnomad SAS
AF:
0.0494
Gnomad FIN
AF:
0.0772
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.0622
Gnomad OTH
AF:
0.0793
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0722
AC:
10989
AN:
152306
Hom.:
729
Cov.:
33
AF XY:
0.0751
AC XY:
5596
AN XY:
74476
show subpopulations
Gnomad4 AFR
AF:
0.0528
Gnomad4 AMR
AF:
0.0691
Gnomad4 ASJ
AF:
0.0377
Gnomad4 EAS
AF:
0.408
Gnomad4 SAS
AF:
0.0495
Gnomad4 FIN
AF:
0.0772
Gnomad4 NFE
AF:
0.0622
Gnomad4 OTH
AF:
0.0781
Alfa
AF:
0.0607
Hom.:
155
Bravo
AF:
0.0751
Asia WGS
AF:
0.190
AC:
659
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.72
CADD
Benign
5.7
DANN
Benign
0.86

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: rs32934; hg19: chr5-76010706; API