Variant rs1421378 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 0.512 in 152,160 control chromosomes in the GnomAD database, including 22,448 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 0.51 ( 22445 hom., cov: 33)

Exomes 𝑓: 0.26 ( 3 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.47

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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 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:

0.512

AC:

77804

AN:

152000

Hom.:

22398

Cov.:

show subpopulations

Gnomad AFR

AF:

0.776

Gnomad AMI

AF:

0.326

Gnomad AMR

AF:

0.513

Gnomad ASJ

AF:

0.526

Gnomad EAS

AF:

0.270

Gnomad SAS

AF:

0.664

Gnomad FIN

AF:

0.352

Gnomad MID

AF:

0.614

Gnomad NFE

AF:

0.385

Gnomad OTH

AF:

0.511

GnomAD4 exome

AF:

0.262

AC:

AN:

Hom.:

AF XY:

0.281

AC XY:

AN XY:

show subpopulations

Gnomad4 EAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.250

Gnomad4 OTH exome

AF:

0.333

GnomAD4 genome

AF:

0.512

AC:

77909

AN:

152118

Hom.:

22445

Cov.:

AF XY:

0.511

AC XY:

37996

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.777

Gnomad4 AMR

AF:

0.513

Gnomad4 ASJ

AF:

0.526

Gnomad4 EAS

AF:

0.269

Gnomad4 SAS

AF:

0.663

Gnomad4 FIN

AF:

0.352

Gnomad4 NFE

AF:

0.385

Gnomad4 OTH

AF:

0.512

Alfa

AF:

0.407

Hom.:

24032

Bravo

AF:

0.528

Asia WGS

AF:

0.529

AC:

1843

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.1

DANN

Benign

0.39

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