6-116784356-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 0.807 in 151,980 control chromosomes in the GnomAD database, including 49,578 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 0.81 ( 49578 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.861
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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.862 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:
0.807
AC:
122548
AN:
151862
Hom.:
49543
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.817
Gnomad AMI
AF:
0.879
Gnomad AMR
AF:
0.816
Gnomad ASJ
AF:
0.927
Gnomad EAS
AF:
0.712
Gnomad SAS
AF:
0.885
Gnomad FIN
AF:
0.770
Gnomad MID
AF:
0.899
Gnomad NFE
AF:
0.798
Gnomad OTH
AF:
0.824
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.807
AC:
122635
AN:
151980
Hom.:
49578
Cov.:
31
AF XY:
0.805
AC XY:
59806
AN XY:
74284
show subpopulations
Gnomad4 AFR
AF:
0.817
Gnomad4 AMR
AF:
0.816
Gnomad4 ASJ
AF:
0.927
Gnomad4 EAS
AF:
0.712
Gnomad4 SAS
AF:
0.884
Gnomad4 FIN
AF:
0.770
Gnomad4 NFE
AF:
0.798
Gnomad4 OTH
AF:
0.822
Alfa
AF:
0.807
Hom.:
67792
Bravo
AF:
0.808
Asia WGS
AF:
0.804
AC:
2793
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.44
DANN
Benign
0.72

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: rs587771; hg19: chr6-117105519; API