rs10511814

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 0.0173 in 152,338 control chromosomes in the GnomAD database, including 59 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 0.017 ( 59 hom., cov: 33)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.115
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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0799 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.27616916A>G intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.0173
AC:
2627
AN:
152220
Hom.:
58
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0249
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0391
Gnomad ASJ
AF:
0.00490
Gnomad EAS
AF:
0.0869
Gnomad SAS
AF:
0.0162
Gnomad FIN
AF:
0.00245
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00585
Gnomad OTH
AF:
0.0129
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0173
AC:
2634
AN:
152338
Hom.:
59
Cov.:
33
AF XY:
0.0175
AC XY:
1302
AN XY:
74506
show subpopulations
Gnomad4 AFR
AF:
0.0248
Gnomad4 AMR
AF:
0.0393
Gnomad4 ASJ
AF:
0.00490
Gnomad4 EAS
AF:
0.0865
Gnomad4 SAS
AF:
0.0164
Gnomad4 FIN
AF:
0.00245
Gnomad4 NFE
AF:
0.00585
Gnomad4 OTH
AF:
0.0142
Alfa
AF:
0.0134
Hom.:
1
Bravo
AF:
0.0225
Asia WGS
AF:
0.0480
AC:
168
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.3
DANN
Benign
0.45

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: rs10511814; hg19: chr9-27616914; API