rs2876117

chr6-7738698-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001718.6(BMP6):c.664+11079G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 152,122 control chromosomes in the GnomAD database, including 11,367 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.37 (11367 hom., cov: 33)
• Consequence: BMP6 NM_001718.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

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]

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 (NFE) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BMP6	NM_001718.6	c.664+11079G>T		intron_variant		ENST00000283147.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BMP6	ENST00000283147.7	c.664+11079G>T		intron_variant		1	NM_001718.6	P1

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55893 AN: 152004 Hom.: 11369 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.367 AC: 55892 AN: 152122 Hom.: 11367 Cov.: 33 AF XY: 0.366 AC XY: 27239 AN XY: 74366

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.382

Alfa AF: 0.443 Hom.: 14382

Bravo AF: 0.347

Asia WGS AF: 0.353 AC: 1229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.21
Dann	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2876117; hg19: chr6-7738931;