chr14-56058851-G-A

Position:

• chr14-56058851-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.242 in 152,092 control chromosomes in the GnomAD database, including 5,797 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.24 (5797 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.394

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 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: 0.242 AC: 36792 AN: 151974 Hom.: 5795 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.242 AC: 36831 AN: 152092 Hom.: 5797 Cov.: 32 AF XY: 0.248 AC XY: 18413 AN XY: 74354

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.203

Alfa AF: 0.164 Hom.: 6409

Bravo AF: 0.250

Asia WGS AF: 0.402 AC: 1397 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Chronic osteomyelitis Other:1

association, no assertion criteria provided

case-control

Department of Orthopeadics and Traumatology, Nanfang Hospital

Sep 01, 2016

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.69
DANN	Benign	0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs398652; hg19: chr14-56525569;