Variant chr6-156565521-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 0.204 in 152,124 control chromosomes in the GnomAD database, including 3,242 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 0.20 ( 3242 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.603

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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 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:

0.204

AC:

30942

AN:

152006

Hom.:

3235

Cov.:

show subpopulations

Gnomad AFR

AF:

0.226

Gnomad AMI

AF:

0.259

Gnomad AMR

AF:

0.153

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.0922

Gnomad SAS

AF:

0.199

Gnomad FIN

AF:

0.236

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.195

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

GnomAD4 genome

AF:

0.204

AC:

30973

AN:

152124

Hom.:

3242

Cov.:

AF XY:

0.204

AC XY:

15193

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.226

Gnomad4 AMR

AF:

0.154

Gnomad4 ASJ

AF:

0.181

Gnomad4 EAS

AF:

0.0924

Gnomad4 SAS

AF:

0.199

Gnomad4 FIN

AF:

0.236

Gnomad4 NFE

AF:

0.206

Gnomad4 OTH

AF:

0.193

Alfa

AF:

0.204

Hom.:

1644

Bravo

AF:

0.198

Asia WGS

AF:

0.190

AC:

659

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.13

DANN

Benign

0.46

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