Variant chr6-32700749-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 0.295 in 152,072 control chromosomes in the GnomAD database, including 7,067 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 0.30 ( 7067 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.43

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.389 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:

0.295

AC:

44809

AN:

151952

Hom.:

7050

Cov.:

show subpopulations

Gnomad AFR

AF:

0.294

Gnomad AMI

AF:

0.400

Gnomad AMR

AF:

0.397

Gnomad ASJ

AF:

0.325

Gnomad EAS

AF:

0.297

Gnomad SAS

AF:

0.210

Gnomad FIN

AF:

0.466

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.249

Gnomad OTH

AF:

0.292

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

GnomAD4 genome

AF:

0.295

AC:

44872

AN:

152072

Hom.:

7067

Cov.:

AF XY:

0.305

AC XY:

22663

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.294

Gnomad4 AMR

AF:

0.398

Gnomad4 ASJ

AF:

0.325

Gnomad4 EAS

AF:

0.297

Gnomad4 SAS

AF:

0.212

Gnomad4 FIN

AF:

0.466

Gnomad4 NFE

AF:

0.249

Gnomad4 OTH

AF:

0.289

Alfa

AF:

0.270

Hom.:

3443

Bravo

AF:

0.295

Asia WGS

AF:

0.277

AC:

970

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

9.1

DANN

Benign

0.45

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