Variant rs1765805 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 0.697 in 152,074 control chromosomes in the GnomAD database, including 38,499 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 0.70 ( 38499 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.39

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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 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:

0.696

AC:

105823

AN:

151956

Hom.:

38433

Cov.:

show subpopulations

Gnomad AFR

AF:

0.924

Gnomad AMI

AF:

0.658

Gnomad AMR

AF:

0.670

Gnomad ASJ

AF:

0.594

Gnomad EAS

AF:

0.589

Gnomad SAS

AF:

0.630

Gnomad FIN

AF:

0.508

Gnomad MID

AF:

0.570

Gnomad NFE

AF:

0.613

Gnomad OTH

AF:

0.668

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

GnomAD4 genome

AF:

0.697

AC:

105947

AN:

152074

Hom.:

38499

Cov.:

AF XY:

0.688

AC XY:

51161

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.924

Gnomad4 AMR

AF:

0.670

Gnomad4 ASJ

AF:

0.594

Gnomad4 EAS

AF:

0.590

Gnomad4 SAS

AF:

0.629

Gnomad4 FIN

AF:

0.508

Gnomad4 NFE

AF:

0.613

Gnomad4 OTH

AF:

0.670

Alfa

AF:

0.659

Hom.:

3987

Bravo

AF:

0.719

Asia WGS

AF:

0.623

AC:

2167

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.056

DANN

Benign

0.84

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