Variant 22-35394330-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 0.0532 in 152,404 control chromosomes in the GnomAD database, including 257 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 0.053 ( 256 hom., cov: 32)

Exomes 𝑓: 0.022 ( 1 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.838

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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.35394330A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0534

AC:

8077

AN:

151254

Hom.:

256

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0680

Gnomad AMI

AF:

0.0680

Gnomad AMR

AF:

0.0346

Gnomad ASJ

AF:

0.0208

Gnomad EAS

AF:

0.00444

Gnomad SAS

AF:

0.0263

Gnomad FIN

AF:

0.0519

Gnomad MID

AF:

0.0160

Gnomad NFE

AF:

0.0566

Gnomad OTH

AF:

0.0443

GnomAD4 exome

AF:

0.0215

AC:

AN:

1068

Hom.:

AF XY:

0.0236

AC XY:

AN XY:

678

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0119

Gnomad4 NFE exome

AF:

0.0269

Gnomad4 OTH exome

AF:

0.0294

GnomAD4 genome

AF:

0.0534

AC:

8088

AN:

151336

Hom.:

256

Cov.:

AF XY:

0.0522

AC XY:

3855

AN XY:

73818

show subpopulations

Gnomad4 AFR

AF:

0.0682

Gnomad4 AMR

AF:

0.0345

Gnomad4 ASJ

AF:

0.0208

Gnomad4 EAS

AF:

0.00426

Gnomad4 SAS

AF:

0.0264

Gnomad4 FIN

AF:

0.0519

Gnomad4 NFE

AF:

0.0565

Gnomad4 OTH

AF:

0.0435

Alfa

AF:

0.0590

Hom.:

Bravo

AF:

0.0523

Asia WGS

AF:

0.0220

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.1

DANN

Benign

0.69

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