Variant rs4446909 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 0.213 in 547,538 control chromosomes in the GnomAD database, including 13,448 homozygotes. There are 59,167 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 0.18 ( 2901 hom., 12929 hem., cov: 31)

Exomes 𝑓: 0.23 ( 10547 hom. 46238 hem. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.112

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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 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:

0.179

AC:

27110

AN:

151766

Hom.:

2906

Cov.:

AF XY:

0.175

AC XY:

12930

AN XY:

74080

show subpopulations

Gnomad AFR

AF:

0.0446

Gnomad AMI

AF:

0.188

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.283

Gnomad SAS

AF:

0.163

Gnomad FIN

AF:

0.126

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.251

Gnomad OTH

AF:

0.205

GnomAD4 exome

AF:

0.226

AC:

89320

AN:

395654

Hom.:

10547

AF XY:

0.224

AC XY:

46238

AN XY:

206338

show subpopulations

Gnomad4 AFR exome

AF:

0.0457

Gnomad4 AMR exome

AF:

0.199

Gnomad4 ASJ exome

AF:

0.230

Gnomad4 EAS exome

AF:

0.282

Gnomad4 SAS exome

AF:

0.167

Gnomad4 FIN exome

AF:

0.130

Gnomad4 NFE exome

AF:

0.252

Gnomad4 OTH exome

AF:

0.213

GnomAD4 genome

AF:

0.178

AC:

27095

AN:

151884

Hom.:

2901

Cov.:

AF XY:

0.174

AC XY:

12929

AN XY:

74208

show subpopulations

Gnomad4 AFR

AF:

0.0445

Gnomad4 AMR

AF:

0.207

Gnomad4 ASJ

AF:

0.236

Gnomad4 EAS

AF:

0.282

Gnomad4 SAS

AF:

0.164

Gnomad4 FIN

AF:

0.126

Gnomad4 NFE

AF:

0.251

Gnomad4 OTH

AF:

0.202

Bravo

AF:

0.181

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.0

DANN

Benign

0.55

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