Variant 15-74733647-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 0.31 in 151,924 control chromosomes in the GnomAD database, including 9,888 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 0.31 ( 9888 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.921

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=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 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:

0.310

AC:

47008

AN:

151806

Hom.:

9845

Cov.:

show subpopulations

Gnomad AFR

AF:

0.536

Gnomad AMI

AF:

0.251

Gnomad AMR

AF:

0.418

Gnomad ASJ

AF:

0.243

Gnomad EAS

AF:

0.600

Gnomad SAS

AF:

0.373

Gnomad FIN

AF:

0.146

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.301

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

GnomAD4 genome

AF:

0.310

AC:

47127

AN:

151924

Hom.:

9888

Cov.:

AF XY:

0.315

AC XY:

23414

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.536

Gnomad4 AMR

AF:

0.419

Gnomad4 ASJ

AF:

0.243

Gnomad4 EAS

AF:

0.599

Gnomad4 SAS

AF:

0.376

Gnomad4 FIN

AF:

0.146

Gnomad4 NFE

AF:

0.151

Gnomad4 OTH

AF:

0.306

Alfa

AF:

0.199

Hom.:

4046

Bravo

AF:

0.338

Asia WGS

AF:

0.529

AC:

1835

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.68

DANN

Benign

0.12

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