Variant rs1082714 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 0.427 in 151,926 control chromosomes in the GnomAD database, including 16,492 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 0.43 ( 16492 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0150

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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 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:

0.427

AC:

64804

AN:

151808

Hom.:

16457

Cov.:

show subpopulations

Gnomad AFR

AF:

0.710

Gnomad AMI

AF:

0.348

Gnomad AMR

AF:

0.309

Gnomad ASJ

AF:

0.366

Gnomad EAS

AF:

0.581

Gnomad SAS

AF:

0.307

Gnomad FIN

AF:

0.366

Gnomad MID

AF:

0.369

Gnomad NFE

AF:

0.293

Gnomad OTH

AF:

0.381

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

GnomAD4 genome

AF:

0.427

AC:

64885

AN:

151926

Hom.:

16492

Cov.:

AF XY:

0.427

AC XY:

31681

AN XY:

74228

show subpopulations

Gnomad4 AFR

AF:

0.710

Gnomad4 AMR

AF:

0.309

Gnomad4 ASJ

AF:

0.366

Gnomad4 EAS

AF:

0.582

Gnomad4 SAS

AF:

0.306

Gnomad4 FIN

AF:

0.366

Gnomad4 NFE

AF:

0.293

Gnomad4 OTH

AF:

0.378

Alfa

AF:

0.329

Hom.:

6785

Bravo

AF:

0.439

Asia WGS

AF:

0.420

AC:

1461

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.3

DANN

Benign

0.60

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