Variant chr2-236588594-A-G 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 0.374 in 152,092 control chromosomes in the GnomAD database, including 16,919 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 0.37 ( 16919 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.532

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=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 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:

0.374

AC:

56780

AN:

151974

Hom.:

16861

Cov.:

show subpopulations

Gnomad AFR

AF:

0.831

Gnomad AMI

AF:

0.138

Gnomad AMR

AF:

0.219

Gnomad ASJ

AF:

0.204

Gnomad EAS

AF:

0.259

Gnomad SAS

AF:

0.282

Gnomad FIN

AF:

0.128

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.335

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

GnomAD4 genome

AF:

0.374

AC:

56886

AN:

152092

Hom.:

16919

Cov.:

AF XY:

0.365

AC XY:

27156

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.832

Gnomad4 AMR

AF:

0.219

Gnomad4 ASJ

AF:

0.204

Gnomad4 EAS

AF:

0.258

Gnomad4 SAS

AF:

0.281

Gnomad4 FIN

AF:

0.128

Gnomad4 NFE

AF:

0.197

Gnomad4 OTH

AF:

0.332

Alfa

AF:

0.220

Hom.:

7468

Bravo

AF:

0.400

Asia WGS

AF:

0.274

AC:

955

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

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