Variant rs737923 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 0.38 in 1,073,982 control chromosomes in the GnomAD database, including 81,214 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 0.41 ( 13432 hom., cov: 32)

Exomes 𝑓: 0.37 ( 67782 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.54

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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 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:

0.413

AC:

62734

AN:

151970

Hom.:

13390

Cov.:

show subpopulations

Gnomad AFR

AF:

0.461

Gnomad AMI

AF:

0.229

Gnomad AMR

AF:

0.416

Gnomad ASJ

AF:

0.380

Gnomad EAS

AF:

0.690

Gnomad SAS

AF:

0.491

Gnomad FIN

AF:

0.404

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.363

Gnomad OTH

AF:

0.404

GnomAD4 exome

AF:

0.375

AC:

345385

AN:

921894

Hom.:

67782

AF XY:

0.377

AC XY:

170305

AN XY:

451982

show subpopulations

Gnomad4 AFR exome

AF:

0.464

Gnomad4 AMR exome

AF:

0.393

Gnomad4 ASJ exome

AF:

0.379

Gnomad4 EAS exome

AF:

0.736

Gnomad4 SAS exome

AF:

0.459

Gnomad4 FIN exome

AF:

0.390

Gnomad4 NFE exome

AF:

0.353

Gnomad4 OTH exome

AF:

0.390

GnomAD4 genome

AF:

0.413

AC:

62838

AN:

152088

Hom.:

13432

Cov.:

AF XY:

0.419

AC XY:

31123

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.461

Gnomad4 AMR

AF:

0.417

Gnomad4 ASJ

AF:

0.380

Gnomad4 EAS

AF:

0.690

Gnomad4 SAS

AF:

0.491

Gnomad4 FIN

AF:

0.404

Gnomad4 NFE

AF:

0.363

Gnomad4 OTH

AF:

0.411

Alfa

AF:

0.371

Hom.:

11118

Bravo

AF:

0.412

Asia WGS

AF:

0.596

AC:

2071

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.56

DANN

Benign

0.75

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