Variant rs41286572 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 0.0657 in 534,412 control chromosomes in the GnomAD database, including 1,381 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 0.061 ( 342 hom., cov: 32)

Exomes 𝑓: 0.068 ( 1039 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0710

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=-0.6).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
	use as main transcript	n.101059844G>A	intergenic_region
MIR154	NR_029704.1 linkuse as main transcript	n.*6G>A	downstream_gene_variant
MIR154	unassigned_transcript_2438 use as main transcript	n.*18G>A	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MEG9	ENST00000699461.1 linkuse as main transcript	n.382-1649G>A		intron_variant
MIR154	ENST00000385243.1 linkuse as main transcript	n.*6G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.0611

AC:

9289

AN:

152124

Hom.:

341

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0276

Gnomad AMI

AF:

0.189

Gnomad AMR

AF:

0.0587

Gnomad ASJ

AF:

0.0626

Gnomad EAS

AF:

0.0297

Gnomad SAS

AF:

0.0548

Gnomad FIN

AF:

0.0990

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0769

Gnomad OTH

AF:

0.0670

GnomAD3 exomes

AF:

0.0628

AC:

15742

AN:

250856

Hom.:

605

AF XY:

0.0640

AC XY:

8695

AN XY:

135790

show subpopulations

Gnomad AFR exome

AF:

0.0265

Gnomad AMR exome

AF:

0.0328

Gnomad ASJ exome

AF:

0.0558

Gnomad EAS exome

AF:

0.0303

Gnomad SAS exome

AF:

0.0555

Gnomad FIN exome

AF:

0.100

Gnomad NFE exome

AF:

0.0776

Gnomad OTH exome

AF:

0.0649

GnomAD4 exome

AF:

0.0676

AC:

25818

AN:

382170

Hom.:

1039

Cov.:

AF XY:

0.0677

AC XY:

14730

AN XY:

217556

show subpopulations

Gnomad4 AFR exome

AF:

0.0274

Gnomad4 AMR exome

AF:

0.0326

Gnomad4 ASJ exome

AF:

0.0555

Gnomad4 EAS exome

AF:

0.0310

Gnomad4 SAS exome

AF:

0.0558

Gnomad4 FIN exome

AF:

0.0992

Gnomad4 NFE exome

AF:

0.0778

Gnomad4 OTH exome

AF:

0.0707

GnomAD4 genome

AF:

0.0610

AC:

9290

AN:

152242

Hom.:

342

Cov.:

AF XY:

0.0614

AC XY:

4567

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.0276

Gnomad4 AMR

AF:

0.0586

Gnomad4 ASJ

AF:

0.0626

Gnomad4 EAS

AF:

0.0297

Gnomad4 SAS

AF:

0.0553

Gnomad4 FIN

AF:

0.0990

Gnomad4 NFE

AF:

0.0768

Gnomad4 OTH

AF:

0.0653

Alfa

AF:

0.0607

Hom.:

157

Bravo

AF:

0.0554

Asia WGS

AF:

0.0470

AC:

163

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

DANN

Benign

0.90

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