Variant chr6-119991183-G-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 0.267 in 151,970 control chromosomes in the GnomAD database, including 5,723 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 0.27 ( 5723 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.24

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 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:

0.267

AC:

40569

AN:

151852

Hom.:

5720

Cov.:

show subpopulations

Gnomad AFR

AF:

0.237

Gnomad AMI

AF:

0.288

Gnomad AMR

AF:

0.222

Gnomad ASJ

AF:

0.278

Gnomad EAS

AF:

0.549

Gnomad SAS

AF:

0.374

Gnomad FIN

AF:

0.320

Gnomad MID

AF:

0.268

Gnomad NFE

AF:

0.258

Gnomad OTH

AF:

0.271

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

GnomAD4 genome

AF:

0.267

AC:

40585

AN:

151970

Hom.:

5723

Cov.:

AF XY:

0.270

AC XY:

20079

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.237

Gnomad4 AMR

AF:

0.222

Gnomad4 ASJ

AF:

0.278

Gnomad4 EAS

AF:

0.549

Gnomad4 SAS

AF:

0.374

Gnomad4 FIN

AF:

0.320

Gnomad4 NFE

AF:

0.258

Gnomad4 OTH

AF:

0.272

Alfa

AF:

0.263

Hom.:

3288

Bravo

AF:

0.261

Asia WGS

AF:

0.425

AC:

1476

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.66

DANN

Benign

0.64

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