Variant rs9323178 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 0.581 in 152,048 control chromosomes in the GnomAD database, including 27,431 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 0.58 ( 27429 hom., cov: 31)

Exomes 𝑓: 0.50 ( 2 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.413

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 = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.22644437A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.581

AC:

88234

AN:

151914

Hom.:

27393

Cov.:

show subpopulations

Gnomad AFR

AF:

0.809

Gnomad AMI

AF:

0.622

Gnomad AMR

AF:

0.418

Gnomad ASJ

AF:

0.455

Gnomad EAS

AF:

0.274

Gnomad SAS

AF:

0.488

Gnomad FIN

AF:

0.498

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.529

Gnomad OTH

AF:

0.532

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

AF XY:

0.625

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

0.500

GnomAD4 genome

AF:

0.581

AC:

88309

AN:

152034

Hom.:

27429

Cov.:

AF XY:

0.573

AC XY:

42553

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.809

Gnomad4 AMR

AF:

0.417

Gnomad4 ASJ

AF:

0.455

Gnomad4 EAS

AF:

0.274

Gnomad4 SAS

AF:

0.487

Gnomad4 FIN

AF:

0.498

Gnomad4 NFE

AF:

0.529

Gnomad4 OTH

AF:

0.525

Alfa

AF:

0.531

Hom.:

29713

Bravo

AF:

0.581

Asia WGS

AF:

0.363

AC:

1266

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

2.5

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