Variant rs926692 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 0.575 in 152,038 control chromosomes in the GnomAD database, including 26,143 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 0.57 ( 26143 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.312

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 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:

0.575

AC:

87282

AN:

151918

Hom.:

26085

Cov.:

show subpopulations

Gnomad AFR

AF:

0.705

Gnomad AMI

AF:

0.588

Gnomad AMR

AF:

0.656

Gnomad ASJ

AF:

0.459

Gnomad EAS

AF:

0.778

Gnomad SAS

AF:

0.612

Gnomad FIN

AF:

0.464

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.483

Gnomad OTH

AF:

0.551

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

GnomAD4 genome

AF:

0.575

AC:

87398

AN:

152038

Hom.:

26143

Cov.:

AF XY:

0.579

AC XY:

43030

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.705

Gnomad4 AMR

AF:

0.657

Gnomad4 ASJ

AF:

0.459

Gnomad4 EAS

AF:

0.778

Gnomad4 SAS

AF:

0.612

Gnomad4 FIN

AF:

0.464

Gnomad4 NFE

AF:

0.483

Gnomad4 OTH

AF:

0.549

Alfa

AF:

0.538

Hom.:

2820

Bravo

AF:

0.596

Asia WGS

AF:

0.646

AC:

2244

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.7

DANN

Benign

0.50

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