Variant chr14-106686431-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 0.243 in 151,920 control chromosomes in the GnomAD database, including 4,984 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 0.24 ( 4984 hom., cov: 33)

Exomes 𝑓: 0.20 ( 0 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.62

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=-0.99).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 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:

0.243

AC:

36952

AN:

151794

Hom.:

4981

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.222

Gnomad AMR

AF:

0.243

Gnomad ASJ

AF:

0.321

Gnomad EAS

AF:

0.346

Gnomad SAS

AF:

0.492

Gnomad FIN

AF:

0.272

Gnomad MID

AF:

0.308

Gnomad NFE

AF:

0.260

Gnomad OTH

AF:

0.257

GnomAD4 exome

AF:

0.200

AC:

AN:

Hom.:

AF XY:

0.200

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

0.250

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.243

AC:

36973

AN:

151910

Hom.:

4984

Cov.:

AF XY:

0.248

AC XY:

18438

AN XY:

74246

show subpopulations

Gnomad4 AFR

AF:

0.160

Gnomad4 AMR

AF:

0.244

Gnomad4 ASJ

AF:

0.321

Gnomad4 EAS

AF:

0.347

Gnomad4 SAS

AF:

0.491

Gnomad4 FIN

AF:

0.272

Gnomad4 NFE

AF:

0.260

Gnomad4 OTH

AF:

0.255

Alfa

AF:

0.247

Hom.:

1138

Bravo

AF:

0.235

Asia WGS

AF:

0.384

AC:

1337

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

3.5

DANN

Benign

0.44

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