Variant 15-63042489-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1

The variant allele was found at a frequency of 0.181 in 260,850 control chromosomes in the GnomAD database, including 4,638 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.18 ( 2602 hom., cov: 33)

Exomes 𝑓: 0.18 ( 2036 hom. )

Consequence

Unknown

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.14

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.31).

BP6

Variant 15-63042489-G-C is Benign according to our data. Variant chr15-63042489-G-C is described in ClinVar as [Benign]. Clinvar id is 668767.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

27327

AN:

151960

Hom.:

2602

Cov.:

show subpopulations

Gnomad AFR

AF:

0.174

Gnomad AMI

AF:

0.396

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.225

Gnomad EAS

AF:

0.00583

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.245

Gnomad NFE

AF:

0.201

Gnomad OTH

AF:

0.186

GnomAD4 exome

AF:

0.182

AC:

19790

AN:

108780

Hom.:

2036

AF XY:

0.175

AC XY:

10498

AN XY:

59850

show subpopulations

Gnomad4 AFR exome

AF:

0.154

Gnomad4 AMR exome

AF:

0.117

Gnomad4 ASJ exome

AF:

0.234

Gnomad4 EAS exome

AF:

0.00263

Gnomad4 SAS exome

AF:

0.132

Gnomad4 FIN exome

AF:

0.221

Gnomad4 NFE exome

AF:

0.202

Gnomad4 OTH exome

AF:

0.190

GnomAD4 genome

AF:

0.180

AC:

27321

AN:

152070

Hom.:

2602

Cov.:

AF XY:

0.177

AC XY:

13145

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.174

Gnomad4 AMR

AF:

0.126

Gnomad4 ASJ

AF:

0.225

Gnomad4 EAS

AF:

0.00584

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.219

Gnomad4 NFE

AF:

0.201

Gnomad4 OTH

AF:

0.184

Alfa

AF:

0.105

Hom.:

188

Bravo

AF:

0.172

Asia WGS

AF:

0.0640

AC:

225

AN:

3464

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.31

CADD

Benign

DANN

Benign

0.92

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over