rs34706883

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 0.0517 in 152,220 control chromosomes in the GnomAD database, including 336 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 0.052 ( 336 hom., cov: 32)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.732
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=-0.78).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0872 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.27837477A>C intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.0518
AC:
7872
AN:
152102
Hom.:
336
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0140
Gnomad AMI
AF:
0.143
Gnomad AMR
AF:
0.0346
Gnomad ASJ
AF:
0.0196
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.0397
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.0891
Gnomad OTH
AF:
0.0407
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0517
AC:
7868
AN:
152220
Hom.:
336
Cov.:
32
AF XY:
0.0466
AC XY:
3470
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.0139
Gnomad4 AMR
AF:
0.0346
Gnomad4 ASJ
AF:
0.0196
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.0397
Gnomad4 NFE
AF:
0.0890
Gnomad4 OTH
AF:
0.0402
Alfa
AF:
0.0703
Hom.:
463
Bravo
AF:
0.0502
Asia WGS
AF:
0.00433
AC:
16
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
4.9
DANN
Benign
0.25

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: rs34706883; hg19: chr6-27805255; API