Variant rs5946512 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 0.436 in 151,848 control chromosomes in the GnomAD database, including 15,757 homozygotes. There are 32,493 hemizygotes in GnomAD. 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 0.44 ( 15757 hom., 32493 hem., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.190

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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 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:

0.435

AC:

66053

AN:

151730

Hom.:

15722

Cov.:

AF XY:

0.438

AC XY:

32406

AN XY:

74030

show subpopulations

Gnomad AFR

AF:

0.593

Gnomad AMI

AF:

0.203

Gnomad AMR

AF:

0.425

Gnomad ASJ

AF:

0.307

Gnomad EAS

AF:

0.698

Gnomad SAS

AF:

0.499

Gnomad FIN

AF:

0.349

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.343

Gnomad OTH

AF:

0.396

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

GnomAD4 genome

AF:

0.436

AC:

66150

AN:

151848

Hom.:

15757

Cov.:

AF XY:

0.438

AC XY:

32493

AN XY:

74158

show subpopulations

Gnomad4 AFR

AF:

0.593

Gnomad4 AMR

AF:

0.425

Gnomad4 ASJ

AF:

0.307

Gnomad4 EAS

AF:

0.697

Gnomad4 SAS

AF:

0.501

Gnomad4 FIN

AF:

0.349

Gnomad4 NFE

AF:

0.343

Gnomad4 OTH

AF:

0.401

Bravo

AF:

0.448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

4.4

DANN

Benign

0.20

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