Variant 2-66852811-C-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 0.279 in 152,018 control chromosomes in the GnomAD database, including 5,989 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 0.28 ( 5989 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.110

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=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 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:

0.279

AC:

42415

AN:

151898

Hom.:

5985

Cov.:

show subpopulations

Gnomad AFR

AF:

0.246

Gnomad AMI

AF:

0.368

Gnomad AMR

AF:

0.252

Gnomad ASJ

AF:

0.376

Gnomad EAS

AF:

0.171

Gnomad SAS

AF:

0.311

Gnomad FIN

AF:

0.317

Gnomad MID

AF:

0.350

Gnomad NFE

AF:

0.299

Gnomad OTH

AF:

0.271

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

GnomAD4 genome

AF:

0.279

AC:

42457

AN:

152018

Hom.:

5989

Cov.:

AF XY:

0.279

AC XY:

20708

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.247

Gnomad4 AMR

AF:

0.253

Gnomad4 ASJ

AF:

0.376

Gnomad4 EAS

AF:

0.170

Gnomad4 SAS

AF:

0.312

Gnomad4 FIN

AF:

0.317

Gnomad4 NFE

AF:

0.299

Gnomad4 OTH

AF:

0.274

Alfa

AF:

0.284

Hom.:

1104

Bravo

AF:

0.273

Asia WGS

AF:

0.298

AC:

1034

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.6

DANN

Benign

0.28

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