rs2735940

chr5-1296371-A-Gchr5-1296371-A-T

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 0.492 in 152,062 control chromosomes in the GnomAD database, including 18,531 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance,association (no stars).

• Frequency: Genomes: 𝑓 0.49 (18531 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Uncertain significance; association no assertion criteria provided U:1 O:1
• Conservation: PhyloP100: -0.330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.577 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: 0.492 AC: 74689 AN: 151944 Hom.: 18516 Cov.: 33

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.492 AC: 74745 AN: 152062 Hom.: 18531 Cov.: 33 AF XY: 0.493 AC XY: 36693 AN XY: 74358

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.457

Alfa AF: 0.483 Hom.: 4328

Bravo AF: 0.498

Asia WGS AF: 0.434 AC: 1512 AN: 3478

ClinVar

Significance: Uncertain significance; association

Submissions summary: Uncertain:1 Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Coronary artery disease, susceptibility to Uncertain:1

Uncertain significance, no assertion criteria provided

literature only

OMIM

Sep 22, 2006

- -

Chronic osteomyelitis Other:1

association, no assertion criteria provided

case-control

Department of Orthopeadics and Traumatology, Nanfang Hospital

Sep 01, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.58
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2735940; hg19: chr5-1296486;