5-1296371-A-G

Variant names:

• chr5-1296371-A-G
• rs2735940
• ENST00000771252.1:n.690A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000771252.1(ENSG00000300381):​n.690A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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: ENSG00000300381 ENST00000771252.1 non_coding_transcript_exon
• Clinical Significance: Uncertain significance; association no assertion criteria provided U:1 O:1
• Conservation: PhyloP100: -0.330
• Publications: 95 publications found

Genes affected

ENSG00000300381 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000771252.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300381	ENST00000771252.1		n.690A>G		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AF: 0.472 AC: 19578 AN: 41472

American (AMR) AF: 0.587 AC: 8976 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1296 AN: 3466

East Asian (EAS) AF: 0.529 AC: 2727 AN: 5156

South Asian (SAS) AF: 0.351 AC: 1695 AN: 4826

European-Finnish (FIN) AF: 0.530 AC: 5606 AN: 10568

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.491 AC: 33340 AN: 67966

Other (OTH) AF: 0.457 AC: 966 AN: 2114

Alfa AF: 0.491 Hom.: 32560

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.58
DANN	Benign	0.51
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2735940; hg19: chr5-1296486;