Variant rs888419 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 0.411 in 152,154 control chromosomes in the GnomAD database, including 13,900 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 0.41 ( 13900 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.312

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=-0.96).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.488 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:

0.411

AC:

62483

AN:

152034

Hom.:

13892

Cov.:

show subpopulations

Gnomad AFR

AF:

0.269

Gnomad AMI

AF:

0.502

Gnomad AMR

AF:

0.497

Gnomad ASJ

AF:

0.500

Gnomad EAS

AF:

0.134

Gnomad SAS

AF:

0.339

Gnomad FIN

AF:

0.448

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.492

Gnomad OTH

AF:

0.415

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

GnomAD4 genome

AF:

0.411

AC:

62517

AN:

152154

Hom.:

13900

Cov.:

AF XY:

0.411

AC XY:

30551

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.269

Gnomad4 AMR

AF:

0.497

Gnomad4 ASJ

AF:

0.500

Gnomad4 EAS

AF:

0.134

Gnomad4 SAS

AF:

0.338

Gnomad4 FIN

AF:

0.448

Gnomad4 NFE

AF:

0.492

Gnomad4 OTH

AF:

0.420

Alfa

AF:

0.480

Hom.:

17827

Bravo

AF:

0.407

Asia WGS

AF:

0.247

AC:

858

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

4.0

DANN

Benign

0.45

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