Variant chr14-104302812-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 0.347 in 152,178 control chromosomes in the GnomAD database, including 9,284 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 0.35 ( 9284 hom., cov: 34)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.771

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 (AMR) allele frequency at 95% confidence interval = 0.397 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:

0.347

AC:

52776

AN:

152060

Hom.:

9285

Cov.:

show subpopulations

Gnomad AFR

AF:

0.326

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.406

Gnomad ASJ

AF:

0.448

Gnomad EAS

AF:

0.280

Gnomad SAS

AF:

0.231

Gnomad FIN

AF:

0.406

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.347

Gnomad OTH

AF:

0.354

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

GnomAD4 genome

AF:

0.347

AC:

52792

AN:

152178

Hom.:

9284

Cov.:

AF XY:

0.349

AC XY:

25934

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.326

Gnomad4 AMR

AF:

0.405

Gnomad4 ASJ

AF:

0.448

Gnomad4 EAS

AF:

0.279

Gnomad4 SAS

AF:

0.231

Gnomad4 FIN

AF:

0.406

Gnomad4 NFE

AF:

0.347

Gnomad4 OTH

AF:

0.355

Alfa

AF:

0.318

Hom.:

4050

Bravo

AF:

0.351

Asia WGS

AF:

0.272

AC:

947

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

1.1

DANN

Benign

0.80

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