chr10-28677565-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012342.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAMBI	NM_012342.3	MANE Select	c.-333T>G		5_prime_UTR	Exon 1 of 3	NP_036474.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAMBI	ENST00000375533.6	TSL:1 MANE Select	c.-333T>G		5_prime_UTR	Exon 1 of 3	ENSP00000364683.3
	BAMBI	ENST00000497699.1	TSL:2	n.56T>G		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.232 AC: 180 AN: 776

American (AMR) AF: 0.328 AC: 237 AN: 722

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 147 AN: 806

East Asian (EAS) AF: 0.420 AC: 567 AN: 1350

South Asian (SAS) AF: 0.184 AC: 36 AN: 196

European-Finnish (FIN) AF: 0.151 AC: 299 AN: 1978

Middle Eastern (MID) AF: 0.140 AC: 19 AN: 136

European-Non Finnish (NFE) AF: 0.132 AC: 2091 AN: 15884

Other (OTH) AF: 0.175 AC: 282 AN: 1608

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

African (AFR) AF: 0.236 AC: 9760 AN: 41366

American (AMR) AF: 0.284 AC: 4334 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 619 AN: 3464

East Asian (EAS) AF: 0.447 AC: 2273 AN: 5086

South Asian (SAS) AF: 0.211 AC: 1019 AN: 4824

European-Finnish (FIN) AF: 0.173 AC: 1797 AN: 10394

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.124 AC: 8387 AN: 67774

Other (OTH) AF: 0.191 AC: 402 AN: 2102

Alfa AF: 0.117 Hom.: 540

Bravo AF: 0.204

Asia WGS AF: 0.354 AC: 1222 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.7
DANN	Benign	0.38
PhyloP100		-0.31
PromoterAI		0.013	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1888085; hg19: chr10-28966494;