Variant rs924463 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 0.0529 in 152,252 control chromosomes in the GnomAD database, including 241 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 0.053 ( 241 hom., cov: 32)

Exomes 𝑓: 0.13 ( 0 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.583

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=-1.0).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0602 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:

0.0529

AC:

8043

AN:

152126

Hom.:

238

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0459

Gnomad AMI

AF:

0.0504

Gnomad AMR

AF:

0.0607

Gnomad ASJ

AF:

0.0912

Gnomad EAS

AF:

0.00888

Gnomad SAS

AF:

0.0265

Gnomad FIN

AF:

0.0288

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.0618

Gnomad OTH

AF:

0.0684

GnomAD4 exome

AF:

0.125

AC:

AN:

Hom.:

AF XY:

0.125

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

0.125

GnomAD4 genome

AF:

0.0529

AC:

8053

AN:

152244

Hom.:

241

Cov.:

AF XY:

0.0517

AC XY:

3845

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.0461

Gnomad4 AMR

AF:

0.0606

Gnomad4 ASJ

AF:

0.0912

Gnomad4 EAS

AF:

0.00890

Gnomad4 SAS

AF:

0.0265

Gnomad4 FIN

AF:

0.0288

Gnomad4 NFE

AF:

0.0618

Gnomad4 OTH

AF:

0.0681

Alfa

AF:

0.0522

Hom.:

Bravo

AF:

0.0560

Asia WGS

AF:

0.0290

AC:

101

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

1.7

DANN

Benign

0.46

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