GeneBe

rs4290865

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 0.775 in 151,842 control chromosomes in the GnomAD database, including 45,741 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 0.78 ( 45741 hom., cov: 31)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.939
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=-0.98).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.91743550A>C intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.775
AC:
117645
AN:
151724
Hom.:
45735
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.769
Gnomad AMI
AF:
0.743
Gnomad AMR
AF:
0.739
Gnomad ASJ
AF:
0.765
Gnomad EAS
AF:
0.654
Gnomad SAS
AF:
0.704
Gnomad FIN
AF:
0.703
Gnomad MID
AF:
0.788
Gnomad NFE
AF:
0.814
Gnomad OTH
AF:
0.770
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.775
AC:
117694
AN:
151842
Hom.:
45741
Cov.:
31
AF XY:
0.767
AC XY:
56903
AN XY:
74188
show subpopulations
Gnomad4 AFR
AF:
0.768
Gnomad4 AMR
AF:
0.738
Gnomad4 ASJ
AF:
0.765
Gnomad4 EAS
AF:
0.655
Gnomad4 SAS
AF:
0.702
Gnomad4 FIN
AF:
0.703
Gnomad4 NFE
AF:
0.814
Gnomad4 OTH
AF:
0.767
Alfa
AF:
0.794
Hom.:
18551
Bravo
AF:
0.777
Asia WGS
AF:
0.694
AC:
2413
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
3.2
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: rs4290865; hg19: chr4-92664701; API