Variant chr6-115807742-C-T details in Genebe, Genetics Data Aggregator

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 0.234 in 152,000 control chromosomes in the GnomAD database, including 4,365 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 0.23 ( 4365 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.919

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=-0.96).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.234

AC:

35597

AN:

151880

Hom.:

4360

Cov.:

show subpopulations

Gnomad AFR

AF:

0.199

Gnomad AMI

AF:

0.418

Gnomad AMR

AF:

0.191

Gnomad ASJ

AF:

0.313

Gnomad EAS

AF:

0.204

Gnomad SAS

AF:

0.317

Gnomad FIN

AF:

0.183

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.264

Gnomad OTH

AF:

0.232

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.234

AC:

35620

AN:

152000

Hom.:

4365

Cov.:

AF XY:

0.231

AC XY:

17165

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.199

Gnomad4 AMR

AF:

0.191

Gnomad4 ASJ

AF:

0.313

Gnomad4 EAS

AF:

0.204

Gnomad4 SAS

AF:

0.317

Gnomad4 FIN

AF:

0.183

Gnomad4 NFE

AF:

0.264

Gnomad4 OTH

AF:

0.234

Alfa

AF:

0.238

Hom.:

2211

Bravo

AF:

0.230

Asia WGS

AF:

0.246

AC:

854

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.043

DANN

Benign

0.36

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over