Variant rs6038115 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 0.513 in 514,212 control chromosomes in the GnomAD database, including 68,922 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 0.52 ( 20476 hom., cov: 32)

Exomes 𝑓: 0.51 ( 48446 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.198

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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.5280486G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.519

AC:

78768

AN:

151792

Hom.:

20457

Cov.:

show subpopulations

Gnomad AFR

AF:

0.550

Gnomad AMI

AF:

0.445

Gnomad AMR

AF:

0.474

Gnomad ASJ

AF:

0.509

Gnomad EAS

AF:

0.671

Gnomad SAS

AF:

0.569

Gnomad FIN

AF:

0.520

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.496

Gnomad OTH

AF:

0.511

GnomAD3 exomes

AF:

0.516

AC:

116955

AN:

226788

Hom.:

31049

AF XY:

0.520

AC XY:

65147

AN XY:

125354

show subpopulations

Gnomad AFR exome

AF:

0.546

Gnomad AMR exome

AF:

0.449

Gnomad ASJ exome

AF:

0.502

Gnomad EAS exome

AF:

0.675

Gnomad SAS exome

AF:

0.570

Gnomad FIN exome

AF:

0.526

Gnomad NFE exome

AF:

0.492

Gnomad OTH exome

AF:

0.497

GnomAD4 exome

AF:

0.510

AC:

184860

AN:

362302

Hom.:

48446

Cov.:

AF XY:

0.516

AC XY:

107235

AN XY:

207826

show subpopulations

Gnomad4 AFR exome

AF:

0.547

Gnomad4 AMR exome

AF:

0.448

Gnomad4 ASJ exome

AF:

0.499

Gnomad4 EAS exome

AF:

0.665

Gnomad4 SAS exome

AF:

0.568

Gnomad4 FIN exome

AF:

0.512

Gnomad4 NFE exome

AF:

0.489

Gnomad4 OTH exome

AF:

0.513

GnomAD4 genome

AF:

0.519

AC:

78834

AN:

151910

Hom.:

20476

Cov.:

AF XY:

0.522

AC XY:

38725

AN XY:

74228

show subpopulations

Gnomad4 AFR

AF:

0.550

Gnomad4 AMR

AF:

0.474

Gnomad4 ASJ

AF:

0.509

Gnomad4 EAS

AF:

0.671

Gnomad4 SAS

AF:

0.567

Gnomad4 FIN

AF:

0.520

Gnomad4 NFE

AF:

0.496

Gnomad4 OTH

AF:

0.515

Alfa

AF:

0.507

Hom.:

4473

Bravo

AF:

0.514

Asia WGS

AF:

0.601

AC:

2087

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.4

DANN

Benign

0.39

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