Variant rs2001844 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 0.432 in 152,098 control chromosomes in the GnomAD database, including 14,350 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 0.43 ( 14350 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.108

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=-0.65).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 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:

0.432

AC:

65598

AN:

151980

Hom.:

14324

Cov.:

show subpopulations

Gnomad AFR

AF:

0.379

Gnomad AMI

AF:

0.656

Gnomad AMR

AF:

0.365

Gnomad ASJ

AF:

0.370

Gnomad EAS

AF:

0.533

Gnomad SAS

AF:

0.349

Gnomad FIN

AF:

0.468

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.472

Gnomad OTH

AF:

0.420

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

GnomAD4 genome

AF:

0.432

AC:

65661

AN:

152098

Hom.:

14350

Cov.:

AF XY:

0.427

AC XY:

31720

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.380

Gnomad4 AMR

AF:

0.365

Gnomad4 ASJ

AF:

0.370

Gnomad4 EAS

AF:

0.534

Gnomad4 SAS

AF:

0.347

Gnomad4 FIN

AF:

0.468

Gnomad4 NFE

AF:

0.472

Gnomad4 OTH

AF:

0.427

Alfa

AF:

0.445

Hom.:

2227

Bravo

AF:

0.426

Asia WGS

AF:

0.462

AC:

1611

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

DANN

Benign

0.86

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