Genetic Variant BAMBI:c.-333T>G (chr10-28677565-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.314

Publications

4 publications found

Variant links:

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 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAMBI	NM_012342.3 link	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	ENST00000375533.6 link	c.-333T>G		5_prime_UTR_variant	Exon 1 of 3	1	NM_012342.3	ENSP00000364683.3
BAMBI	ENST00000497699.1 link	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.:

show subpopulations

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.:

AF XY:

0.166

AC XY:

2063

AN XY:

12452

show subpopulations

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:

AN:

196

European-Finnish (FIN)

AF:

0.151

AC:

299

AN:

1978

Middle Eastern (MID)

AF:

0.140

AC:

AN:

136

European-Non Finnish (NFE)

AF:

0.132

AC:

2091

AN:

15884

Other (OTH)

AF:

0.175

AC:

282

AN:

1608

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

151

302

453

604

755

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.189

AC:

28649

AN:

151458

Hom.:

3237

Cov.:

AF XY:

0.196

AC XY:

14483

AN XY:

74032

show subpopulations

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:

AN:

292

European-Non Finnish (NFE)

AF:

0.124

AC:

8387

AN:

67774

Other (OTH)

AF:

0.191

AC:

402

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1139

2277

3416

4554

5693

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

306

612

918

1224

1530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

7.7

(source)

DANN

Benign

0.38

PhyloP100

-0.31

PromoterAI

0.013

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over