Variant rs2219994 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 0.102 in 152,064 control chromosomes in the GnomAD database, including 2,225 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 0.10 ( 2225 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.197

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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15435

AN:

151946

Hom.:

2208

Cov.:

show subpopulations

Gnomad AFR

AF:

0.319

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0441

Gnomad ASJ

AF:

0.0432

Gnomad EAS

AF:

0.00868

Gnomad SAS

AF:

0.0114

Gnomad FIN

AF:

0.0191

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0142

Gnomad OTH

AF:

0.0872

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

GnomAD4 genome

AF:

0.102

AC:

15495

AN:

152064

Hom.:

2225

Cov.:

AF XY:

0.0995

AC XY:

7399

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.319

Gnomad4 AMR

AF:

0.0440

Gnomad4 ASJ

AF:

0.0432

Gnomad4 EAS

AF:

0.00870

Gnomad4 SAS

AF:

0.0110

Gnomad4 FIN

AF:

0.0191

Gnomad4 NFE

AF:

0.0142

Gnomad4 OTH

AF:

0.0863

Alfa

AF:

0.0536

Hom.:

225

Bravo

AF:

0.114

Asia WGS

AF:

0.0360

AC:

127

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.3

DANN

Benign

0.58

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