Variant chr18-28455130-A-T 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 0.251 in 152,148 control chromosomes in the GnomAD database, including 5,013 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 0.25 ( 5013 hom., cov: 33)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.158

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=-0.99).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.28455130A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.252

AC:

38239

AN:

152030

Hom.:

5019

Cov.:

show subpopulations

Gnomad AFR

AF:

0.183

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.251

Gnomad ASJ

AF:

0.241

Gnomad EAS

AF:

0.178

Gnomad SAS

AF:

0.332

Gnomad FIN

AF:

0.302

Gnomad MID

AF:

0.213

Gnomad NFE

AF:

0.286

Gnomad OTH

AF:

0.260

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

GnomAD4 genome

AF:

0.251

AC:

38239

AN:

152148

Hom.:

5013

Cov.:

AF XY:

0.253

AC XY:

18813

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.183

Gnomad4 AMR

AF:

0.251

Gnomad4 ASJ

AF:

0.241

Gnomad4 EAS

AF:

0.178

Gnomad4 SAS

AF:

0.330

Gnomad4 FIN

AF:

0.302

Gnomad4 NFE

AF:

0.286

Gnomad4 OTH

AF:

0.257

Alfa

AF:

0.145

Hom.:

280

Bravo

AF:

0.241

Asia WGS

AF:

0.234

AC:

815

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.86

DANN

Benign

0.43

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