6-32713854-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 0.67 in 152,052 control chromosomes in the GnomAD database, including 34,584 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 0.67 ( 34584 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.45
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.670
AC:
101775
AN:
151934
Hom.:
34560
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.651
Gnomad AMI
AF:
0.784
Gnomad AMR
AF:
0.759
Gnomad ASJ
AF:
0.792
Gnomad EAS
AF:
0.858
Gnomad SAS
AF:
0.766
Gnomad FIN
AF:
0.665
Gnomad MID
AF:
0.785
Gnomad NFE
AF:
0.631
Gnomad OTH
AF:
0.714
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.670
AC:
101849
AN:
152052
Hom.:
34584
Cov.:
32
AF XY:
0.674
AC XY:
50112
AN XY:
74316
show subpopulations
Gnomad4 AFR
AF:
0.650
Gnomad4 AMR
AF:
0.760
Gnomad4 ASJ
AF:
0.792
Gnomad4 EAS
AF:
0.858
Gnomad4 SAS
AF:
0.765
Gnomad4 FIN
AF:
0.665
Gnomad4 NFE
AF:
0.631
Gnomad4 OTH
AF:
0.717
Alfa
AF:
0.656
Hom.:
49171
Bravo
AF:
0.679
Asia WGS
AF:
0.837
AC:
2912
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
1.2
DANN
Benign
0.62

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: rs9275596; hg19: chr6-32681631; API