Variant 15-94727238-C-T 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 0.614 in 151,944 control chromosomes in the GnomAD database, including 28,946 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 0.61 ( 28946 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.02

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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.614

AC:

93201

AN:

151826

Hom.:

28929

Cov.:

show subpopulations

Gnomad AFR

AF:

0.542

Gnomad AMI

AF:

0.614

Gnomad AMR

AF:

0.669

Gnomad ASJ

AF:

0.741

Gnomad EAS

AF:

0.682

Gnomad SAS

AF:

0.745

Gnomad FIN

AF:

0.539

Gnomad MID

AF:

0.699

Gnomad NFE

AF:

0.635

Gnomad OTH

AF:

0.631

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

GnomAD4 genome

AF:

0.614

AC:

93265

AN:

151944

Hom.:

28946

Cov.:

AF XY:

0.615

AC XY:

45679

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.542

Gnomad4 AMR

AF:

0.669

Gnomad4 ASJ

AF:

0.741

Gnomad4 EAS

AF:

0.683

Gnomad4 SAS

AF:

0.747

Gnomad4 FIN

AF:

0.539

Gnomad4 NFE

AF:

0.635

Gnomad4 OTH

AF:

0.626

Alfa

AF:

0.644

Hom.:

72152

Bravo

AF:

0.622

Asia WGS

AF:

0.689

AC:

2395

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

DANN

Benign

0.45

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