Variant rs12417955 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 0.535 in 517,910 control chromosomes in the GnomAD database, including 74,904 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 0.54 ( 22376 hom., cov: 33)

Exomes 𝑓: 0.53 ( 52528 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.553

Variant links:

Genes affected

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.1262997A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.540

AC:

82030

AN:

151880

Hom.:

22342

Cov.:

show subpopulations

Gnomad AFR

AF:

0.558

Gnomad AMI

AF:

0.558

Gnomad AMR

AF:

0.591

Gnomad ASJ

AF:

0.542

Gnomad EAS

AF:

0.667

Gnomad SAS

AF:

0.513

Gnomad FIN

AF:

0.587

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.502

Gnomad OTH

AF:

0.545

GnomAD3 exomes

AF:

0.549

AC:

125515

AN:

228708

Hom.:

34900

AF XY:

0.541

AC XY:

68118

AN XY:

125952

show subpopulations

Gnomad AFR exome

AF:

0.559

Gnomad AMR exome

AF:

0.622

Gnomad ASJ exome

AF:

0.544

Gnomad EAS exome

AF:

0.671

Gnomad SAS exome

AF:

0.509

Gnomad FIN exome

AF:

0.576

Gnomad NFE exome

AF:

0.509

Gnomad OTH exome

AF:

0.542

GnomAD4 exome

AF:

0.533

AC:

194950

AN:

365912

Hom.:

52528

Cov.:

AF XY:

0.526

AC XY:

109335

AN XY:

207946

show subpopulations

Gnomad4 AFR exome

AF:

0.559

Gnomad4 AMR exome

AF:

0.622

Gnomad4 ASJ exome

AF:

0.539

Gnomad4 EAS exome

AF:

0.673

Gnomad4 SAS exome

AF:

0.508

Gnomad4 FIN exome

AF:

0.575

Gnomad4 NFE exome

AF:

0.507

Gnomad4 OTH exome

AF:

0.528

GnomAD4 genome

AF:

0.540

AC:

82116

AN:

151998

Hom.:

22376

Cov.:

AF XY:

0.546

AC XY:

40529

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.559

Gnomad4 AMR

AF:

0.592

Gnomad4 ASJ

AF:

0.542

Gnomad4 EAS

AF:

0.667

Gnomad4 SAS

AF:

0.512

Gnomad4 FIN

AF:

0.587

Gnomad4 NFE

AF:

0.502

Gnomad4 OTH

AF:

0.548

Alfa

AF:

0.512

Hom.:

10280

Bravo

AF:

0.543

Asia WGS

AF:

0.622

AC:

2165

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.7

DANN

Benign

0.49

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