Variant 4-15935462-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 0.412 in 152,888 control chromosomes in the GnomAD database, including 13,945 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 0.41 ( 13877 hom., cov: 33)

Exomes 𝑓: 0.40 ( 68 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.157

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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 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:

0.412

AC:

62573

AN:

151956

Hom.:

13866

Cov.:

show subpopulations

Gnomad AFR

AF:

0.262

Gnomad AMI

AF:

0.319

Gnomad AMR

AF:

0.440

Gnomad ASJ

AF:

0.400

Gnomad EAS

AF:

0.581

Gnomad SAS

AF:

0.268

Gnomad FIN

AF:

0.590

Gnomad MID

AF:

0.442

Gnomad NFE

AF:

0.468

Gnomad OTH

AF:

0.421

GnomAD4 exome

AF:

0.402

AC:

327

AN:

814

Hom.:

AF XY:

0.366

AC XY:

145

AN XY:

396

show subpopulations

Gnomad4 AFR exome

AF:

0.167

Gnomad4 AMR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.321

Gnomad4 EAS exome

AF:

0.750

Gnomad4 SAS exome

AF:

0.167

Gnomad4 FIN exome

AF:

0.550

Gnomad4 NFE exome

AF:

0.398

Gnomad4 OTH exome

AF:

0.447

GnomAD4 genome

AF:

0.412

AC:

62600

AN:

152074

Hom.:

13877

Cov.:

AF XY:

0.417

AC XY:

30978

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.262

Gnomad4 AMR

AF:

0.441

Gnomad4 ASJ

AF:

0.400

Gnomad4 EAS

AF:

0.581

Gnomad4 SAS

AF:

0.269

Gnomad4 FIN

AF:

0.590

Gnomad4 NFE

AF:

0.468

Gnomad4 OTH

AF:

0.416

Alfa

AF:

0.404

Hom.:

2866

Bravo

AF:

0.398

Asia WGS

AF:

0.376

AC:

1308

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.4

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over