rs2735940

Variant names:

• chr5-1296371-A-G
• rs2735940

Your query was ambiguous. Multiple possible variants found:

• chr5-1296371-A-G
• chr5-1296371-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

Sep 22, 2006

OMIM

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: literature only

- -

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

- -

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;