10-28679377-A-G

Position:

• chr10-28679377-A-G

Variant summary

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

The NM_012342.3(BAMBI):​c.76+1404A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 152,142 control chromosomes in the GnomAD database, including 42,801 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 0.74 (42801 hom., cov: 33)
• Consequence: BAMBI NM_012342.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.98

Genes affected

BAMBI (HGNC:30251): (BMP and activin membrane bound inhibitor) This gene encodes a transmembrane glycoprotein related to the type I receptors of the transforming growth factor-beta (TGF-beta) family, whose members play important roles in signal transduction in many developmental and pathological processes. The encoded protein however is a pseudoreceptor, lacking an intracellular serine/threonine kinase domain required for signaling. Similar proteins in frog, mouse and zebrafish function as negative regulators of TGF-beta, which has led to the suggestion that the encoded protein may function to limit the signaling range of the TGF-beta family during early embryogenesis. [provided by RefSeq, Jul 2008]

BAMBI (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BAMBI	NM_012342.3	c.76+1404A>G		intron_variant		ENST00000375533.6	NP_036474.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BAMBI	ENST00000375533.6	c.76+1404A>G		intron_variant		1	NM_012342.3	ENSP00000364683.3
BAMBI	ENST00000497699.1	n.464+1404A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112754 AN: 152024 Hom.: 42748 Cov.: 33

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.742 AC: 112857 AN: 152142 Hom.: 42801 Cov.: 33 AF XY: 0.747 AC XY: 55559 AN XY: 74374

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.746

Alfa AF: 0.687 Hom.: 6234

Bravo AF: 0.756

Asia WGS AF: 0.901 AC: 3134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	17
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: rs675558; hg19: chr10-28968306;