10-129466317-T-G

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 0.702 in 151,938 control chromosomes in the GnomAD database, including 40,750 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 0.70 ( 40750 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.792
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.702
AC:
106642
AN:
151820
Hom.:
40742
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.375
Gnomad AMI
AF:
0.853
Gnomad AMR
AF:
0.798
Gnomad ASJ
AF:
0.821
Gnomad EAS
AF:
0.980
Gnomad SAS
AF:
0.867
Gnomad FIN
AF:
0.763
Gnomad MID
AF:
0.769
Gnomad NFE
AF:
0.829
Gnomad OTH
AF:
0.736
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.702
AC:
106671
AN:
151938
Hom.:
40750
Cov.:
31
AF XY:
0.705
AC XY:
52357
AN XY:
74220
show subpopulations
Gnomad4 AFR
AF:
0.374
Gnomad4 AMR
AF:
0.798
Gnomad4 ASJ
AF:
0.821
Gnomad4 EAS
AF:
0.981
Gnomad4 SAS
AF:
0.867
Gnomad4 FIN
AF:
0.763
Gnomad4 NFE
AF:
0.829
Gnomad4 OTH
AF:
0.737
Alfa
AF:
0.759
Hom.:
12023
Bravo
AF:
0.690
Asia WGS
AF:
0.876
AC:
3046
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
5.5
DANN
Benign
0.42

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: rs1711646; hg19: chr10-131264581; API