Variant chr2-240369088-G-A 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 0.263 in 152,114 control chromosomes in the GnomAD database, including 6,600 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 0.26 ( 6600 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.25

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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 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:

0.263

AC:

39999

AN:

151996

Hom.:

6603

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0949

Gnomad AMI

AF:

0.323

Gnomad AMR

AF:

0.243

Gnomad ASJ

AF:

0.279

Gnomad EAS

AF:

0.0162

Gnomad SAS

AF:

0.153

Gnomad FIN

AF:

0.350

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.381

Gnomad OTH

AF:

0.283

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

GnomAD4 genome

AF:

0.263

AC:

39993

AN:

152114

Hom.:

6600

Cov.:

AF XY:

0.258

AC XY:

19167

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.0947

Gnomad4 AMR

AF:

0.243

Gnomad4 ASJ

AF:

0.279

Gnomad4 EAS

AF:

0.0163

Gnomad4 SAS

AF:

0.154

Gnomad4 FIN

AF:

0.350

Gnomad4 NFE

AF:

0.381

Gnomad4 OTH

AF:

0.279

Alfa

AF:

0.343

Hom.:

11236

Bravo

AF:

0.246

Asia WGS

AF:

0.0870

AC:

304

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.6

DANN

Benign

0.75

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