chr10-28677565-T-G

Variant names:

• chr10-28677565-T-G
• rs1888085
• NM_012342.3:c.-333T>G

Variant summary

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

The NM_012342.3(BAMBI):​c.-333T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 174,914 control chromosomes in the GnomAD database, including 3,633 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 0.19 (3237 hom., cov: 32)
  • Exomes 𝑓: 0.16 (396 hom.)
• Consequence: BAMBI NM_012342.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAMBI	NM_012342.3	c.-333T>G		5_prime_UTR_variant	Exon 1 of 3	ENST00000375533.6	NP_036474.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAMBI	ENST00000375533	c.-333T>G		5_prime_UTR_variant	Exon 1 of 3	1	NM_012342.3	ENSP00000364683.3
BAMBI	ENST00000497699.1	n.56T>G		non_coding_transcript_exon_variant	Exon 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28570 AN: 151348 Hom.: 3207 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.0177

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.182

GnomAD4 exome AF: 0.164 AC: 3858 AN: 23456 Hom.: 396 Cov.: 0 AF XY: 0.166 AC XY: 2063 AN XY: 12452

Gnomad4 AFR exome AF: 0.232

Gnomad4 AMR exome AF: 0.328

Gnomad4 ASJ exome AF: 0.182

Gnomad4 EAS exome AF: 0.420

Gnomad4 SAS exome AF: 0.184

Gnomad4 FIN exome AF: 0.151

Gnomad4 NFE exome AF: 0.132

Gnomad4 OTH exome AF: 0.175

GnomAD4 genome AF: 0.189 AC: 28649 AN: 151458 Hom.: 3237 Cov.: 32 AF XY: 0.196 AC XY: 14483 AN XY: 74032

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.191

Alfa AF: 0.106 Hom.: 266

Bravo AF: 0.204

Asia WGS AF: 0.354 AC: 1222 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.7
DANN	Benign	0.38

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: rs1888085; hg19: chr10-28966494;