GeneBe

6-32460508-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 0.668 in 152,056 control chromosomes in the GnomAD database, including 34,257 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 0.67 ( 34257 hom., cov: 32)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.269
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=-0.96).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.32460508C>T intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HLA-DRB9ENST00000449413.1 linkuse as main transcriptn.77-421G>A intron_variant 6

Frequencies

GnomAD3 genomes
AF:
0.668
AC:
101450
AN:
151938
Hom.:
34227
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.613
Gnomad AMI
AF:
0.762
Gnomad AMR
AF:
0.706
Gnomad ASJ
AF:
0.715
Gnomad EAS
AF:
0.619
Gnomad SAS
AF:
0.576
Gnomad FIN
AF:
0.799
Gnomad MID
AF:
0.535
Gnomad NFE
AF:
0.679
Gnomad OTH
AF:
0.677
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.668
AC:
101523
AN:
152056
Hom.:
34257
Cov.:
32
AF XY:
0.668
AC XY:
49671
AN XY:
74336
show subpopulations
Gnomad4 AFR
AF:
0.613
Gnomad4 AMR
AF:
0.706
Gnomad4 ASJ
AF:
0.715
Gnomad4 EAS
AF:
0.621
Gnomad4 SAS
AF:
0.577
Gnomad4 FIN
AF:
0.799
Gnomad4 NFE
AF:
0.679
Gnomad4 OTH
AF:
0.672
Alfa
AF:
0.673
Hom.:
63331
Bravo
AF:
0.666
Asia WGS
AF:
0.598
AC:
2084
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
4.9
DANN
Benign
0.66

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: rs6903608; hg19: chr6-32428285; API