Variant rs255406 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 0.773 in 147,410 control chromosomes in the GnomAD database, including 44,088 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 0.77 ( 44088 hom., cov: 22)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.875

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.03).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.63478387A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.773

AC:

113857

AN:

147302

Hom.:

44054

Cov.:

show subpopulations

Gnomad AFR

AF:

0.775

Gnomad AMI

AF:

0.855

Gnomad AMR

AF:

0.769

Gnomad ASJ

AF:

0.723

Gnomad EAS

AF:

0.880

Gnomad SAS

AF:

0.761

Gnomad FIN

AF:

0.788

Gnomad MID

AF:

0.711

Gnomad NFE

AF:

0.765

Gnomad OTH

AF:

0.770

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

GnomAD4 genome

AF:

0.773

AC:

113932

AN:

147410

Hom.:

44088

Cov.:

AF XY:

0.774

AC XY:

55389

AN XY:

71556

show subpopulations

Gnomad4 AFR

AF:

0.775

Gnomad4 AMR

AF:

0.769

Gnomad4 ASJ

AF:

0.723

Gnomad4 EAS

AF:

0.880

Gnomad4 SAS

AF:

0.761

Gnomad4 FIN

AF:

0.788

Gnomad4 NFE

AF:

0.765

Gnomad4 OTH

AF:

0.772

Alfa

AF:

0.768

Hom.:

7191

Bravo

AF:

0.775

Asia WGS

AF:

0.811

AC:

2818

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

3.6

DANN

Benign

0.44

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