chr6-129741572-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 0.483 in 152,066 control chromosomes in the GnomAD database, including 17,864 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 0.48 ( 17864 hom., cov: 32)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.99
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=-1.0).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.129741572T>C intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.483
AC:
73453
AN:
151946
Hom.:
17848
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.505
Gnomad AMI
AF:
0.408
Gnomad AMR
AF:
0.502
Gnomad ASJ
AF:
0.448
Gnomad EAS
AF:
0.495
Gnomad SAS
AF:
0.524
Gnomad FIN
AF:
0.435
Gnomad MID
AF:
0.500
Gnomad NFE
AF:
0.472
Gnomad OTH
AF:
0.484
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.483
AC:
73518
AN:
152066
Hom.:
17864
Cov.:
32
AF XY:
0.483
AC XY:
35913
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.505
Gnomad4 AMR
AF:
0.501
Gnomad4 ASJ
AF:
0.448
Gnomad4 EAS
AF:
0.495
Gnomad4 SAS
AF:
0.524
Gnomad4 FIN
AF:
0.435
Gnomad4 NFE
AF:
0.472
Gnomad4 OTH
AF:
0.485
Alfa
AF:
0.469
Hom.:
23254
Bravo
AF:
0.486
Asia WGS
AF:
0.496
AC:
1730
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
0.065
DANN
Benign
0.40

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: rs208869; hg19: chr6-130062717; API