rs398652

Variant names:

• chr14-56058851-G-A
• rs398652

Your query was ambiguous. Multiple possible variants found:

• chr14-56058851-G-A
• chr14-56058851-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.370 AC: 15365 AN: 41476

American (AMR) AF: 0.240 AC: 3673 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3468

East Asian (EAS) AF: 0.645 AC: 3342 AN: 5182

South Asian (SAS) AF: 0.246 AC: 1186 AN: 4820

European-Finnish (FIN) AF: 0.267 AC: 2819 AN: 10570

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9416 AN: 67980

Other (OTH) AF: 0.203 AC: 428 AN: 2112

Alfa AF: 0.179 Hom.: 11885

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

Sep 01, 2016

Department of Orthopeadics and Traumatology, Nanfang Hospital

Significance: association

Review Status: no assertion criteria provided

Collection Method: case-control

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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
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs398652; hg19: chr14-56525569;