Variant rs3218123 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

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 0.057 ( 218 hom., cov: 9)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.76

Variant links:

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ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

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:

0.00

AC:

1684

AN:

29420

Hom.:

219

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00819

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.0437

Gnomad ASJ

AF:

0.197

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.206

Gnomad FIN

AF:

0.0266

Gnomad MID

AF:

0.0281

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.0469

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

Hom.:

AF XY:

0.00

AC XY:

AN XY:

Gnomad4 AFR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0569

AC:

1676

AN:

29470

Hom.:

218

Cov.:

AF XY:

0.0484

AC XY:

779

AN XY:

16100

show subpopulations

Gnomad4 AFR

AF:

0.00805

Gnomad4 AMR

AF:

0.0434

Gnomad4 ASJ

AF:

0.197

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.201

Gnomad4 FIN

AF:

0.0266

Gnomad4 NFE

AF:

0.142

Gnomad4 OTH

AF:

0.0455

Alfa

AF:

0.00283

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

DANN

Benign

0.91

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