Variant 22-28803802-G-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 0.115 in 151,920 control chromosomes in the GnomAD database, including 1,497 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 0.11 ( 1497 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.171

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=-0.69).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.28803802G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000226471	ENST00000418292.1 linkuse as main transcript	n.34+3065G>T	intron_variant	3
ENSG00000226471	ENST00000451486.5 linkuse as main transcript	n.103+1808G>T	intron_variant	5
ENSG00000226471	ENST00000458080.1 linkuse as main transcript	n.55+3065G>T	intron_variant	3

Frequencies

GnomAD3 genomes

AF:

0.115

AC:

17423

AN:

151802

Hom.:

1491

Cov.:

show subpopulations

Gnomad AFR

AF:

0.227

Gnomad AMI

AF:

0.0537

Gnomad AMR

AF:

0.103

Gnomad ASJ

AF:

0.0707

Gnomad EAS

AF:

0.276

Gnomad SAS

AF:

0.0646

Gnomad FIN

AF:

0.0630

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0526

Gnomad OTH

AF:

0.0962

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

GnomAD4 genome

AF:

0.115

AC:

17470

AN:

151920

Hom.:

1497

Cov.:

AF XY:

0.114

AC XY:

8485

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.227

Gnomad4 AMR

AF:

0.104

Gnomad4 ASJ

AF:

0.0707

Gnomad4 EAS

AF:

0.277

Gnomad4 SAS

AF:

0.0648

Gnomad4 FIN

AF:

0.0630

Gnomad4 NFE

AF:

0.0526

Gnomad4 OTH

AF:

0.0994

Alfa

AF:

0.0498

Hom.:

123

Bravo

AF:

0.125

Asia WGS

AF:

0.188

AC:

652

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

8.5

DANN

Benign

0.84

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