Variant chr15-46360969-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 0.473 in 151,554 control chromosomes in the GnomAD database, including 17,977 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 0.47 ( 17977 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.780

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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 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:

0.473

AC:

71657

AN:

151436

Hom.:

17979

Cov.:

show subpopulations

Gnomad AFR

AF:

0.360

Gnomad AMI

AF:

0.637

Gnomad AMR

AF:

0.422

Gnomad ASJ

AF:

0.613

Gnomad EAS

AF:

0.230

Gnomad SAS

AF:

0.424

Gnomad FIN

AF:

0.504

Gnomad MID

AF:

0.592

Gnomad NFE

AF:

0.560

Gnomad OTH

AF:

0.487

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

GnomAD4 genome

AF:

0.473

AC:

71683

AN:

151554

Hom.:

17977

Cov.:

AF XY:

0.468

AC XY:

34606

AN XY:

73998

show subpopulations

Gnomad4 AFR

AF:

0.360

Gnomad4 AMR

AF:

0.421

Gnomad4 ASJ

AF:

0.613

Gnomad4 EAS

AF:

0.230

Gnomad4 SAS

AF:

0.425

Gnomad4 FIN

AF:

0.504

Gnomad4 NFE

AF:

0.560

Gnomad4 OTH

AF:

0.482

Alfa

AF:

0.513

Hom.:

2939

Bravo

AF:

0.463

Asia WGS

AF:

0.307

AC:

1066

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.50

DANN

Benign

0.34

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