9-25501299-T-C

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 0.914 in 152,212 control chromosomes in the GnomAD database, including 64,585 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 0.91 ( 64585 hom., cov: 33)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.80
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=-1.01).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.25501299T>C intergenic_region
LOC107987056XR_001746637.2 linkuse as main transcriptn.271-22934A>G intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.914
AC:
139061
AN:
152094
Hom.:
64558
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.732
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.958
Gnomad ASJ
AF:
0.984
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
0.994
Gnomad FIN
AF:
0.978
Gnomad MID
AF:
0.965
Gnomad NFE
AF:
0.988
Gnomad OTH
AF:
0.932
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.914
AC:
139140
AN:
152212
Hom.:
64585
Cov.:
33
AF XY:
0.916
AC XY:
68194
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.732
Gnomad4 AMR
AF:
0.958
Gnomad4 ASJ
AF:
0.984
Gnomad4 EAS
AF:
1.00
Gnomad4 SAS
AF:
0.994
Gnomad4 FIN
AF:
0.978
Gnomad4 NFE
AF:
0.988
Gnomad4 OTH
AF:
0.933
Alfa
AF:
0.896
Hom.:
4618
Bravo
AF:
0.904
Asia WGS
AF:
0.980
AC:
3406
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
0.98
DANN
Benign
0.70

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: rs2210430; hg19: chr9-25501297; API