chr6-81283434-G-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 0.0527 in 151,662 control chromosomes in the GnomAD database, including 569 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 0.053 ( 569 hom., cov: 32)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.93
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.81283434G>T intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.0527
AC:
7985
AN:
151544
Hom.:
565
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0103
Gnomad AMI
AF:
0.00439
Gnomad AMR
AF:
0.139
Gnomad ASJ
AF:
0.0324
Gnomad EAS
AF:
0.322
Gnomad SAS
AF:
0.167
Gnomad FIN
AF:
0.0503
Gnomad MID
AF:
0.0190
Gnomad NFE
AF:
0.0331
Gnomad OTH
AF:
0.0466
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0527
AC:
8000
AN:
151662
Hom.:
569
Cov.:
32
AF XY:
0.0596
AC XY:
4418
AN XY:
74090
show subpopulations
Gnomad4 AFR
AF:
0.0103
Gnomad4 AMR
AF:
0.140
Gnomad4 ASJ
AF:
0.0324
Gnomad4 EAS
AF:
0.322
Gnomad4 SAS
AF:
0.166
Gnomad4 FIN
AF:
0.0503
Gnomad4 NFE
AF:
0.0331
Gnomad4 OTH
AF:
0.0485
Alfa
AF:
0.0385
Hom.:
239
Bravo
AF:
0.0567
Asia WGS
AF:
0.241
AC:
835
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.23
DANN
Benign
0.48

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: rs9361780; hg19: chr6-81993151; COSMIC: COSV68670116; API