Variant 22-47263264-C-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 0.0626 in 152,324 control chromosomes in the GnomAD database, including 361 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 0.063 ( 361 hom., cov: 33)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.58

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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.47263264C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0627

AC:

9541

AN:

152206

Hom.:

361

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0188

Gnomad AMI

AF:

0.0515

Gnomad AMR

AF:

0.0686

Gnomad ASJ

AF:

0.0942

Gnomad EAS

AF:

0.115

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.0608

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0796

Gnomad OTH

AF:

0.0685

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

GnomAD4 genome

AF:

0.0626

AC:

9535

AN:

152324

Hom.:

361

Cov.:

AF XY:

0.0625

AC XY:

4655

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.0188

Gnomad4 AMR

AF:

0.0686

Gnomad4 ASJ

AF:

0.0942

Gnomad4 EAS

AF:

0.114

Gnomad4 SAS

AF:

0.105

Gnomad4 FIN

AF:

0.0608

Gnomad4 NFE

AF:

0.0796

Gnomad4 OTH

AF:

0.0682

Alfa

AF:

0.0326

Hom.:

Bravo

AF:

0.0606

Asia WGS

AF:

0.131

AC:

459

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

0.16

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