Variant chr6-41186912-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 0.289 in 152,070 control chromosomes in the GnomAD database, including 6,516 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 0.29 ( 6516 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.33

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=-0.99).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.353 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:

0.289

AC:

43921

AN:

151952

Hom.:

6515

Cov.:

show subpopulations

Gnomad AFR

AF:

0.224

Gnomad AMI

AF:

0.295

Gnomad AMR

AF:

0.360

Gnomad ASJ

AF:

0.301

Gnomad EAS

AF:

0.344

Gnomad SAS

AF:

0.337

Gnomad FIN

AF:

0.312

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.301

Gnomad OTH

AF:

0.291

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

GnomAD4 genome

AF:

0.289

AC:

43949

AN:

152070

Hom.:

6516

Cov.:

AF XY:

0.293

AC XY:

21769

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.224

Gnomad4 AMR

AF:

0.361

Gnomad4 ASJ

AF:

0.301

Gnomad4 EAS

AF:

0.343

Gnomad4 SAS

AF:

0.338

Gnomad4 FIN

AF:

0.312

Gnomad4 NFE

AF:

0.301

Gnomad4 OTH

AF:

0.288

Alfa

AF:

0.299

Hom.:

11272

Bravo

AF:

0.289

Asia WGS

AF:

0.365

AC:

1269

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.053

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.

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