GeneBe

rs5906754

Positions:

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 0.516 in 110,102 control chromosomes in the GnomAD database, including 11,948 homozygotes. There are 16,526 hemizygotes in GnomAD. 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 0.52 ( 11948 hom., 16526 hem., cov: 22)

Consequence


intergenic_region

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.245
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.49203767C>T intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.516
AC:
56774
AN:
110047
Hom.:
11956
Cov.:
22
AF XY:
0.511
AC XY:
16505
AN XY:
32311
show subpopulations
Gnomad AFR
AF:
0.243
Gnomad AMI
AF:
0.631
Gnomad AMR
AF:
0.435
Gnomad ASJ
AF:
0.788
Gnomad EAS
AF:
0.333
Gnomad SAS
AF:
0.668
Gnomad FIN
AF:
0.613
Gnomad MID
AF:
0.712
Gnomad NFE
AF:
0.666
Gnomad OTH
AF:
0.543
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.516
AC:
56764
AN:
110102
Hom.:
11948
Cov.:
22
AF XY:
0.510
AC XY:
16526
AN XY:
32376
show subpopulations
Gnomad4 AFR
AF:
0.242
Gnomad4 AMR
AF:
0.435
Gnomad4 ASJ
AF:
0.788
Gnomad4 EAS
AF:
0.333
Gnomad4 SAS
AF:
0.671
Gnomad4 FIN
AF:
0.613
Gnomad4 NFE
AF:
0.666
Gnomad4 OTH
AF:
0.547
Alfa
AF:
0.568
Hom.:
3343
Bravo
AF:
0.486

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
4.8

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: rs5906754; hg19: chrX-49060227; API