dbSNP rs985409033: B3GNT9:p.Arg40* (chr16-67150368-G-A) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_033309.3(B3GNT9):c.118C>T(p.Arg40*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

B3GNT9
NM_033309.3 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0170

Publications

0 publications found

Variant links:

Genes affected

B3GNT9 (HGNC:28714): (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9) Predicted to enable UDP-glycosyltransferase activity. Predicted to be involved in poly-N-acetyllactosamine biosynthetic process. Predicted to be integral component of membrane. Predicted to be active in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

B3GNT9 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GNT9	NM_033309.3 link	c.118C>T	p.Arg40*	stop_gained	Exon 2 of 2	ENST00000449549.4	NP_171608.2	Q6UX72

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GNT9	ENST00000449549.4 link	c.118C>T	p.Arg40*	stop_gained	Exon 2 of 2	1	NM_033309.3	ENSP00000400157.3		Q6UX72

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1195884

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

576558

African (AFR)

AF:

0.00

AC:

AN:

23672

American (AMR)

AF:

0.00

AC:

AN:

9278

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

16172

East Asian (EAS)

AF:

0.00

AC:

AN:

27344

South Asian (SAS)

AF:

0.00

AC:

AN:

44974

European-Finnish (FIN)

AF:

0.00

AC:

AN:

39496

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3330

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

982854

Other (OTH)

AF:

0.00

AC:

AN:

48764

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Uncertain

0.018

BayesDel_noAF

Benign

-0.21

CADD

Pathogenic

(source)

DANN

Benign

0.91

Eigen

Benign

-0.48

Eigen_PC

Benign

-0.85

FATHMM_MKL

Benign

0.025

PhyloP100

0.017

Vest4

0.061

GERP RS

-2.2

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over