rs537332654

Variant names:

• chr6-7727289-GAGCAGCAGCAGCAGC-G
• rs537332654
• NM_001718.6:c.341_355delAGCAGCAGCAGCAGC

Your query was ambiguous. Multiple possible variants found:

• chr6-7727289-GAGCAGCAGCAGCAGC-G
• chr6-7727289-GAGCAGCAGCAGCAGC-GAGC
• chr6-7727289-GAGCAGCAGCAGCAGC-GAGCAGC
• chr6-7727289-GAGCAGCAGCAGCAGC-GAGCAGCAGC
• chr6-7727289-GAGCAGCAGCAGCAGC-GAGCAGCAGCAGC
• chr6-7727289-GAGCAGCAGCAGCAGC-GAGCAGCAGCAGCAGCAGC
• chr6-7727289-GAGCAGCAGCAGCAGC-GAGCAGCAGCAGCAGCAGCAGC
• chr6-7727289-GAGCAGCAGCAGCAGC-GAGCAGCAGCAGCAGCAGCAGCAGC
• chr6-7727289-GAGCAGCAGCAGCAGC-GAGCAGCAGCAGCAGCAGCAGCAGCAGC
• chr6-7727289-GAGCAGCAGCAGCAGC-GAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGC

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001718.6(BMP6):​c.341_355delAGCAGCAGCAGCAGC​(p.Gln114_Gln118del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BMP6 NM_001718.6 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 3 publications found

Genes affected

BMP6 (HGNC:1073): (bone morphogenetic protein 6) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer. This protein regulates a wide range of biological processes including iron homeostasis, fat and bone development, and ovulation. Differential expression of this gene may be associated with progression of breast and prostate cancer. Mutations in this gene may be associated with iron overload in human patients. [provided by RefSeq, Jul 2016]

BMP6 Gene-Disease associations (from GenCC):

• hemochromatosis type 5

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• iron overload, susceptibility to

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001718.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BMP6	NM_001718.6	MANE Select	c.341_355delAGCAGCAGCAGCAGC	p.Gln114_Gln118del	disruptive_inframe_deletion	Exon 1 of 7	NP_001709.1	P22004

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BMP6	ENST00000283147.7	TSL:1 MANE Select	c.341_355delAGCAGCAGCAGCAGC	p.Gln114_Gln118del	disruptive_inframe_deletion	Exon 1 of 7	ENSP00000283147.6	P22004
	BMP6	ENST00000946083.1		c.341_355delAGCAGCAGCAGCAGC	p.Gln114_Gln118del	disruptive_inframe_deletion	Exon 1 of 7	ENSP00000616142.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 4

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs537332654; hg19: chr6-7727522;