Variant rs5946324 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 0.263 in 151,508 control chromosomes in the GnomAD database, including 5,892 homozygotes. There are 19,511 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 0.26 ( 5892 hom., 19511 hem., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.296

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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 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:

0.264

AC:

39915

AN:

151390

Hom.:

5893

Cov.:

AF XY:

0.264

AC XY:

19499

AN XY:

73880

show subpopulations

Gnomad AFR

AF:

0.210

Gnomad AMI

AF:

0.387

Gnomad AMR

AF:

0.198

Gnomad ASJ

AF:

0.399

Gnomad EAS

AF:

0.0211

Gnomad SAS

AF:

0.212

Gnomad FIN

AF:

0.366

Gnomad MID

AF:

0.280

Gnomad NFE

AF:

0.309

Gnomad OTH

AF:

0.251

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

GnomAD4 genome

AF:

0.263

AC:

39916

AN:

151508

Hom.:

5892

Cov.:

AF XY:

0.264

AC XY:

19511

AN XY:

74008

show subpopulations

Gnomad4 AFR

AF:

0.210

Gnomad4 AMR

AF:

0.197

Gnomad4 ASJ

AF:

0.399

Gnomad4 EAS

AF:

0.0211

Gnomad4 SAS

AF:

0.212

Gnomad4 FIN

AF:

0.366

Gnomad4 NFE

AF:

0.309

Gnomad4 OTH

AF:

0.249

Bravo

AF:

0.247

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.13

DANN

Benign

0.33

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