Variant 14-74204553-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 0.404 in 152,014 control chromosomes in the GnomAD database, including 13,444 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 0.40 ( 13444 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.175

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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 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:

0.405

AC:

61443

AN:

151896

Hom.:

13435

Cov.:

show subpopulations

Gnomad AFR

AF:

0.294

Gnomad AMI

AF:

0.296

Gnomad AMR

AF:

0.416

Gnomad ASJ

AF:

0.458

Gnomad EAS

AF:

0.0595

Gnomad SAS

AF:

0.283

Gnomad FIN

AF:

0.504

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.488

Gnomad OTH

AF:

0.406

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

GnomAD4 genome

AF:

0.404

AC:

61476

AN:

152014

Hom.:

13444

Cov.:

AF XY:

0.403

AC XY:

29953

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.294

Gnomad4 AMR

AF:

0.416

Gnomad4 ASJ

AF:

0.458

Gnomad4 EAS

AF:

0.0592

Gnomad4 SAS

AF:

0.283

Gnomad4 FIN

AF:

0.504

Gnomad4 NFE

AF:

0.488

Gnomad4 OTH

AF:

0.409

Alfa

AF:

0.460

Hom.:

33185

Bravo

AF:

0.390

Asia WGS

AF:

0.233

AC:

812

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.2

DANN

Benign

0.30

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