Variant rs1633769 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 0.615 in 152,170 control chromosomes in the GnomAD database, including 31,423 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 0.61 ( 31423 hom., cov: 34)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.46

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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.743 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:

0.615

AC:

93470

AN:

152050

Hom.:

31406

Cov.:

show subpopulations

Gnomad AFR

AF:

0.325

Gnomad AMI

AF:

0.887

Gnomad AMR

AF:

0.652

Gnomad ASJ

AF:

0.718

Gnomad EAS

AF:

0.614

Gnomad SAS

AF:

0.759

Gnomad FIN

AF:

0.702

Gnomad MID

AF:

0.717

Gnomad NFE

AF:

0.748

Gnomad OTH

AF:

0.652

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

GnomAD4 genome

AF:

0.615

AC:

93510

AN:

152170

Hom.:

31423

Cov.:

AF XY:

0.617

AC XY:

45905

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.325

Gnomad4 AMR

AF:

0.652

Gnomad4 ASJ

AF:

0.718

Gnomad4 EAS

AF:

0.614

Gnomad4 SAS

AF:

0.758

Gnomad4 FIN

AF:

0.702

Gnomad4 NFE

AF:

0.748

Gnomad4 OTH

AF:

0.657

Alfa

AF:

0.658

Hom.:

4323

Bravo

AF:

0.596

Asia WGS

AF:

0.669

AC:

2329

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.81

DANN

Benign

0.21

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