Variant rs2095388 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 0.288 in 152,058 control chromosomes in the GnomAD database, including 6,461 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 0.29 ( 6461 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0300

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=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.387 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:

0.288

AC:

43759

AN:

151938

Hom.:

6459

Cov.:

show subpopulations

Gnomad AFR

AF:

0.281

Gnomad AMI

AF:

0.253

Gnomad AMR

AF:

0.395

Gnomad ASJ

AF:

0.316

Gnomad EAS

AF:

0.302

Gnomad SAS

AF:

0.243

Gnomad FIN

AF:

0.211

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.338

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

GnomAD4 genome

AF:

0.288

AC:

43785

AN:

152058

Hom.:

6461

Cov.:

AF XY:

0.287

AC XY:

21351

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.281

Gnomad4 AMR

AF:

0.396

Gnomad4 ASJ

AF:

0.316

Gnomad4 EAS

AF:

0.302

Gnomad4 SAS

AF:

0.242

Gnomad4 FIN

AF:

0.211

Gnomad4 NFE

AF:

0.279

Gnomad4 OTH

AF:

0.336

Alfa

AF:

0.281

Hom.:

2905

Bravo

AF:

0.308

Asia WGS

AF:

0.256

AC:

889

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

DANN

Benign

0.68

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