6-7840548-T-A

Position:

• chr6-7840548-T-A

Variant summary

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

The NM_001718.6(BMP6):​c.665-4592T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,970 control chromosomes in the GnomAD database, including 13,293 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 0.41 (13293 hom., cov: 31)
• Consequence: BMP6 NM_001718.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BMP6	NM_001718.6	c.665-4592T>A		intron_variant		ENST00000283147.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BMP6	ENST00000283147.7	c.665-4592T>A		intron_variant		1	NM_001718.6	P1

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61922 AN: 151850 Hom.: 13276 Cov.: 31

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.408 AC: 61977 AN: 151970 Hom.: 13293 Cov.: 31 AF XY: 0.414 AC XY: 30780 AN XY: 74274

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.402

Alfa AF: 0.378 Hom.: 1398

Bravo AF: 0.417

Asia WGS AF: 0.587 AC: 2041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.0
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs267188; hg19: chr6-7840781;