Variant 4-186067699-A-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 0.176 in 152,184 control chromosomes in the GnomAD database, including 2,473 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 0.18 ( 2473 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.362

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.193 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:

0.176

AC:

26738

AN:

152066

Hom.:

2469

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.309

Gnomad AMR

AF:

0.175

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.204

Gnomad SAS

AF:

0.168

Gnomad FIN

AF:

0.182

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.192

Gnomad OTH

AF:

0.174

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

GnomAD4 genome

AF:

0.176

AC:

26768

AN:

152184

Hom.:

2473

Cov.:

AF XY:

0.176

AC XY:

13081

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.144

Gnomad4 AMR

AF:

0.175

Gnomad4 ASJ

AF:

0.159

Gnomad4 EAS

AF:

0.203

Gnomad4 SAS

AF:

0.167

Gnomad4 FIN

AF:

0.182

Gnomad4 NFE

AF:

0.192

Gnomad4 OTH

AF:

0.175

Alfa

AF:

0.179

Hom.:

328

Bravo

AF:

0.173

Asia WGS

AF:

0.177

AC:

614

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.29

DANN

Benign

0.70

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