10-109471430-C-T

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 0.162 in 151,910 control chromosomes in the GnomAD database, including 6,272 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 0.16 ( 6272 hom., cov: 32)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0350
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=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.109471430C>T intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.162
AC:
24583
AN:
151794
Hom.:
6237
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.545
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0663
Gnomad ASJ
AF:
0.0104
Gnomad EAS
AF:
0.00212
Gnomad SAS
AF:
0.0394
Gnomad FIN
AF:
0.000757
Gnomad MID
AF:
0.0823
Gnomad NFE
AF:
0.00820
Gnomad OTH
AF:
0.122
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.162
AC:
24668
AN:
151910
Hom.:
6272
Cov.:
32
AF XY:
0.157
AC XY:
11655
AN XY:
74280
show subpopulations
Gnomad4 AFR
AF:
0.546
Gnomad4 AMR
AF:
0.0661
Gnomad4 ASJ
AF:
0.0104
Gnomad4 EAS
AF:
0.00213
Gnomad4 SAS
AF:
0.0383
Gnomad4 FIN
AF:
0.000757
Gnomad4 NFE
AF:
0.00820
Gnomad4 OTH
AF:
0.121
Alfa
AF:
0.0979
Hom.:
454
Bravo
AF:
0.185
Asia WGS
AF:
0.0650
AC:
225
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
5.8
DANN
Benign
0.23

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: rs10509897; hg19: chr10-111231188; API