Variant rs1773766 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 0.0795 in 152,412 control chromosomes in the GnomAD database, including 815 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 0.080 ( 815 hom., cov: 33)

Exomes 𝑓: 0.016 ( 0 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.658

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 (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.223143343C>A		intergenic_region
LOC124904522	XR_007066895.1 linkuse as main transcript	n.-12C>A		upstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0793

AC:

12073

AN:

152168

Hom.:

809

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0389

Gnomad ASJ

AF:

0.0314

Gnomad EAS

AF:

0.0939

Gnomad SAS

AF:

0.0532

Gnomad FIN

AF:

0.0298

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0410

Gnomad OTH

AF:

0.0578

GnomAD4 exome

AF:

0.0159

AC:

AN:

126

Hom.:

AF XY:

0.0204

AC XY:

AN XY:

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:

0.00

Gnomad4 NFE exome

AF:

0.0200

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0795

AC:

12111

AN:

152286

Hom.:

815

Cov.:

AF XY:

0.0787

AC XY:

5862

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.179

Gnomad4 AMR

AF:

0.0387

Gnomad4 ASJ

AF:

0.0314

Gnomad4 EAS

AF:

0.0938

Gnomad4 SAS

AF:

0.0536

Gnomad4 FIN

AF:

0.0298

Gnomad4 NFE

AF:

0.0409

Gnomad4 OTH

AF:

0.0572

Alfa

AF:

0.0169

Hom.:

Bravo

AF:

0.0847

Asia WGS

AF:

0.0650

AC:

227

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

5.2

DANN

Benign

0.59

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