Variant chr14-59583538-G-A 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 0.513 in 152,062 control chromosomes in the GnomAD database, including 23,026 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 0.51 ( 23026 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.344

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 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:

0.513

AC:

77978

AN:

151944

Hom.:

23028

Cov.:

show subpopulations

Gnomad AFR

AF:

0.205

Gnomad AMI

AF:

0.691

Gnomad AMR

AF:

0.558

Gnomad ASJ

AF:

0.553

Gnomad EAS

AF:

0.845

Gnomad SAS

AF:

0.568

Gnomad FIN

AF:

0.717

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.625

Gnomad OTH

AF:

0.526

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

GnomAD4 genome

AF:

0.513

AC:

78005

AN:

152062

Hom.:

23026

Cov.:

AF XY:

0.523

AC XY:

38874

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.206

Gnomad4 AMR

AF:

0.557

Gnomad4 ASJ

AF:

0.553

Gnomad4 EAS

AF:

0.845

Gnomad4 SAS

AF:

0.569

Gnomad4 FIN

AF:

0.717

Gnomad4 NFE

AF:

0.625

Gnomad4 OTH

AF:

0.532

Alfa

AF:

0.586

Hom.:

12681

Bravo

AF:

0.488

Asia WGS

AF:

0.688

AC:

2392

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.5

DANN

Benign

0.48

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