Variant rs12800641 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 0.167 in 148,886 control chromosomes in the GnomAD database, including 2,822 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 0.17 ( 2822 hom., cov: 28)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.74442195G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000254631	ENST00000533008.1 linkuse as main transcript	n.155-41982G>A		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

24880

AN:

148768

Hom.:

2812

Cov.:

show subpopulations

Gnomad AFR

AF:

0.300

Gnomad AMI

AF:

0.129

Gnomad AMR

AF:

0.120

Gnomad ASJ

AF:

0.267

Gnomad EAS

AF:

0.0502

Gnomad SAS

AF:

0.188

Gnomad FIN

AF:

0.0523

Gnomad MID

AF:

0.260

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.177

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

GnomAD4 genome

AF:

0.167

AC:

24920

AN:

148886

Hom.:

2822

Cov.:

AF XY:

0.163

AC XY:

11843

AN XY:

72630

show subpopulations

Gnomad4 AFR

AF:

0.300

Gnomad4 AMR

AF:

0.120

Gnomad4 ASJ

AF:

0.267

Gnomad4 EAS

AF:

0.0499

Gnomad4 SAS

AF:

0.189

Gnomad4 FIN

AF:

0.0523

Gnomad4 NFE

AF:

0.120

Gnomad4 OTH

AF:

0.175

Alfa

AF:

0.136

Hom.:

1803

Bravo

AF:

0.185

Asia WGS

AF:

0.132

AC:

457

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.33

DANN

Benign

0.26

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