Variant rs1751725 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 0.0796 in 109,217 control chromosomes in the GnomAD database, including 449 homozygotes. There are 2,669 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 0.080 ( 449 hom., 2669 hem., cov: 21)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.241

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=-0.8).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.281 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:

0.0794

AC:

8671

AN:

109172

Hom.:

448

Cov.:

AF XY:

0.0837

AC XY:

2654

AN XY:

31702

show subpopulations

Gnomad AFR

AF:

0.0401

Gnomad AMI

AF:

0.0237

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.0519

Gnomad EAS

AF:

0.287

Gnomad SAS

AF:

0.299

Gnomad FIN

AF:

0.0476

Gnomad MID

AF:

0.0216

Gnomad NFE

AF:

0.0607

Gnomad OTH

AF:

0.0853

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

GnomAD4 genome

AF:

0.0796

AC:

8689

AN:

109217

Hom.:

449

Cov.:

AF XY:

0.0840

AC XY:

2669

AN XY:

31757

show subpopulations

Gnomad4 AFR

AF:

0.0402

Gnomad4 AMR

AF:

0.198

Gnomad4 ASJ

AF:

0.0519

Gnomad4 EAS

AF:

0.287

Gnomad4 SAS

AF:

0.299

Gnomad4 FIN

AF:

0.0476

Gnomad4 NFE

AF:

0.0607

Gnomad4 OTH

AF:

0.0897

Alfa

AF:

0.0191

Hom.:

Bravo

AF:

0.0876

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.0

DANN

Benign

0.93

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