Variant rs2512449 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 0.48 in 150,000 control chromosomes in the GnomAD database, including 20,037 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 0.48 ( 20037 hom., cov: 26)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.35

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 (AFR) allele frequency at 95% confidence interval = 0.759 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:

0.480

AC:

71897

AN:

149886

Hom.:

19988

Cov.:

show subpopulations

Gnomad AFR

AF:

0.766

Gnomad AMI

AF:

0.382

Gnomad AMR

AF:

0.454

Gnomad ASJ

AF:

0.392

Gnomad EAS

AF:

0.631

Gnomad SAS

AF:

0.530

Gnomad FIN

AF:

0.333

Gnomad MID

AF:

0.436

Gnomad NFE

AF:

0.325

Gnomad OTH

AF:

0.452

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

GnomAD4 genome

AF:

0.480

AC:

71999

AN:

150000

Hom.:

20037

Cov.:

AF XY:

0.482

AC XY:

35216

AN XY:

73112

show subpopulations

Gnomad4 AFR

AF:

0.767

Gnomad4 AMR

AF:

0.455

Gnomad4 ASJ

AF:

0.392

Gnomad4 EAS

AF:

0.631

Gnomad4 SAS

AF:

0.528

Gnomad4 FIN

AF:

0.333

Gnomad4 NFE

AF:

0.325

Gnomad4 OTH

AF:

0.457

Alfa

AF:

0.258

Hom.:

649

Bravo

AF:

0.497

Asia WGS

AF:

0.593

AC:

2044

AN:

3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.51

DANN

Benign

0.40

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