Variant rs4950926 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 0.282 in 152,128 control chromosomes in the GnomAD database, including 7,596 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 0.28 ( 7575 hom., cov: 30)

Exomes 𝑓: 0.38 ( 21 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.405

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=-0.77).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.396 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:

0.282

AC:

42757

AN:

151762

Hom.:

7572

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0884

Gnomad AMI

AF:

0.642

Gnomad AMR

AF:

0.259

Gnomad ASJ

AF:

0.365

Gnomad EAS

AF:

0.0259

Gnomad SAS

AF:

0.214

Gnomad FIN

AF:

0.403

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.400

Gnomad OTH

AF:

0.306

GnomAD4 exome

AF:

0.383

AC:

AN:

248

Hom.:

AF XY:

0.390

AC XY:

AN XY:

172

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.250

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.419

Gnomad4 NFE exome

AF:

0.396

Gnomad4 OTH exome

AF:

0.333

GnomAD4 genome

AF:

0.282

AC:

42761

AN:

151880

Hom.:

7575

Cov.:

AF XY:

0.281

AC XY:

20855

AN XY:

74214

show subpopulations

Gnomad4 AFR

AF:

0.0884

Gnomad4 AMR

AF:

0.258

Gnomad4 ASJ

AF:

0.365

Gnomad4 EAS

AF:

0.0260

Gnomad4 SAS

AF:

0.214

Gnomad4 FIN

AF:

0.403

Gnomad4 NFE

AF:

0.400

Gnomad4 OTH

AF:

0.302

Alfa

AF:

0.297

Hom.:

1115

Bravo

AF:

0.264

Asia WGS

AF:

0.109

AC:

383

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

DANN

Benign

0.83

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