rs7838961

Positions:

• chr8-22181439-G-A
• chr8-22181439-G-C

Variant summary

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

The NM_006129.5(BMP1):​c.1077+956G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 152,018 control chromosomes in the GnomAD database, including 24,050 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 0.56 (24050 hom., cov: 32)
• Consequence: BMP1 NM_006129.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

BMP1 (HGNC:1067): (bone morphogenetic protein 1) This gene encodes a protein that is capable of inducing formation of cartilage in vivo. Although other bone morphogenetic proteins are members of the TGF-beta superfamily, this gene encodes a protein that is not closely related to other known growth factors. This gene is expressed as alternatively spliced variants that share an N-terminal protease domain but differ in their C-terminal region. [provided by RefSeq, Aug 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BMP1	NM_001199.4	c.1077+956G>A		intron_variant		ENST00000306349.13
BMP1	NM_006129.5	c.1077+956G>A		intron_variant		ENST00000306385.10
BMP1	NR_033403.2	n.1148+956G>A		intron_variant, non_coding_transcript_variant
BMP1	NR_033404.2	n.1148+956G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BMP1	ENST00000306349.13	c.1077+956G>A		intron_variant		1	NM_001199.4
BMP1	ENST00000306385.10	c.1077+956G>A		intron_variant		1	NM_006129.5	P1

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84572 AN: 151900 Hom.: 24004 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.557 AC: 84666 AN: 152018 Hom.: 24050 Cov.: 32 AF XY: 0.562 AC XY: 41776 AN XY: 74286

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.569

Alfa AF: 0.497 Hom.: 25252

Bravo AF: 0.561

Asia WGS AF: 0.632 AC: 2196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.98
DANN	Benign	0.48

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: rs7838961; hg19: chr8-22038952;