Variant rs9449067 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 0.618 in 217,572 control chromosomes in the GnomAD database, including 43,059 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 0.63 ( 31650 hom., cov: 31)

Exomes 𝑓: 0.58 ( 11409 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.412

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
	use as main transcript	n.80555778C>A	intergenic_region
LOC648934	use as main transcript	n.80555778C>A	intragenic_variant
LOC112267962	XR_002956360.2 linkuse as main transcript	n.91-24535C>A	intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.632

AC:

95957

AN:

151768

Hom.:

31599

Cov.:

show subpopulations

Gnomad AFR

AF:

0.829

Gnomad AMI

AF:

0.470

Gnomad AMR

AF:

0.631

Gnomad ASJ

AF:

0.634

Gnomad EAS

AF:

0.671

Gnomad SAS

AF:

0.713

Gnomad FIN

AF:

0.461

Gnomad MID

AF:

0.614

Gnomad NFE

AF:

0.533

Gnomad OTH

AF:

0.635

GnomAD4 exome

AF:

0.584

AC:

38376

AN:

65684

Hom.:

11409

AF XY:

0.583

AC XY:

21778

AN XY:

37374

show subpopulations

Gnomad4 AFR exome

AF:

0.848

Gnomad4 AMR exome

AF:

0.685

Gnomad4 ASJ exome

AF:

0.648

Gnomad4 EAS exome

AF:

0.665

Gnomad4 SAS exome

AF:

0.721

Gnomad4 FIN exome

AF:

0.486

Gnomad4 NFE exome

AF:

0.552

Gnomad4 OTH exome

AF:

0.560

GnomAD4 genome

AF:

0.632

AC:

96068

AN:

151888

Hom.:

31650

Cov.:

AF XY:

0.632

AC XY:

46875

AN XY:

74216

show subpopulations

Gnomad4 AFR

AF:

0.829

Gnomad4 AMR

AF:

0.632

Gnomad4 ASJ

AF:

0.634

Gnomad4 EAS

AF:

0.671

Gnomad4 SAS

AF:

0.713

Gnomad4 FIN

AF:

0.461

Gnomad4 NFE

AF:

0.533

Gnomad4 OTH

AF:

0.632

Alfa

AF:

0.496

Hom.:

2207

Bravo

AF:

0.651

Asia WGS

AF:

0.700

AC:

2434

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

5.4

DANN

Benign

0.45

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