Variant rs2142672 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 0.415 in 151,832 control chromosomes in the GnomAD database, including 15,871 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 0.42 ( 15871 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.17

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=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 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:

0.415

AC:

62979

AN:

151714

Hom.:

15822

Cov.:

show subpopulations

Gnomad AFR

AF:

0.692

Gnomad AMI

AF:

0.306

Gnomad AMR

AF:

0.370

Gnomad ASJ

AF:

0.308

Gnomad EAS

AF:

0.737

Gnomad SAS

AF:

0.346

Gnomad FIN

AF:

0.244

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.274

Gnomad OTH

AF:

0.365

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

GnomAD4 genome

AF:

0.415

AC:

63086

AN:

151832

Hom.:

15871

Cov.:

AF XY:

0.412

AC XY:

30569

AN XY:

74216

show subpopulations

Gnomad4 AFR

AF:

0.692

Gnomad4 AMR

AF:

0.370

Gnomad4 ASJ

AF:

0.308

Gnomad4 EAS

AF:

0.737

Gnomad4 SAS

AF:

0.345

Gnomad4 FIN

AF:

0.244

Gnomad4 NFE

AF:

0.274

Gnomad4 OTH

AF:

0.369

Alfa

AF:

0.296

Hom.:

12708

Bravo

AF:

0.437

Asia WGS

AF:

0.590

AC:

2051

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

0.38

DANN

Benign

0.30

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