Variant rs186682 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

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 0.023 ( 11 hom., cov: 0)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.351

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=-0.92).

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.023 (758/33028) while in subpopulation SAS AF= 0.0369 (35/948). AF 95% confidence interval is 0.0273. There are 11 homozygotes in gnomad4. There are 379 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 11 gene

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:

0.0230

AC:

758

AN:

32986

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0302

Gnomad AMI

AF:

0.00446

Gnomad AMR

AF:

0.0213

Gnomad ASJ

AF:

0.0313

Gnomad EAS

AF:

0.00931

Gnomad SAS

AF:

0.0371

Gnomad FIN

AF:

0.0329

Gnomad MID

AF:

0.0536

Gnomad NFE

AF:

0.0192

Gnomad OTH

AF:

0.0332

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

GnomAD4 genome

AF:

0.0230

AC:

758

AN:

33028

Hom.:

Cov.:

AF XY:

0.0240

AC XY:

379

AN XY:

15788

show subpopulations

Gnomad4 AFR

AF:

0.0301

Gnomad4 AMR

AF:

0.0213

Gnomad4 ASJ

AF:

0.0313

Gnomad4 EAS

AF:

0.00934

Gnomad4 SAS

AF:

0.0369

Gnomad4 FIN

AF:

0.0329

Gnomad4 NFE

AF:

0.0192

Gnomad4 OTH

AF:

0.0318

Alfa

AF:

0.291

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.57

DANN

Benign

0.23

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