rs7313849

Variant names:

• chr12-502428-T-C
• rs7313849
• NM_173593.4:c.170-32738T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173593.4(B4GALNT3):​c.170-32738T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,960 control chromosomes in the GnomAD database, including 6,237 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 0.24 (6237 hom., cov: 31)
• Consequence: B4GALNT3 NM_173593.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495
• Publications: 6 publications found

Genes affected

B4GALNT3 (HGNC:24137): (beta-1,4-N-acetyl-galactosaminyltransferase 3) B4GALNT3 transfers N-acetylgalactosamine (GalNAc) onto glucosyl residues to form N,N-prime-diacetyllactosediamine (LacdiNAc, or LDN), a unique terminal structure of cell surface N-glycans (Ikehara et al., 2006 [PubMed 16728562]).[supplied by OMIM, Aug 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B4GALNT3	NM_173593.4	c.170-32738T>C		intron_variant	Intron 1 of 19	ENST00000266383.10	NP_775864.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B4GALNT3	ENST00000266383.10	c.170-32738T>C		intron_variant	Intron 1 of 19	1	NM_173593.4	ENSP00000266383.5
B4GALNT3	ENST00000535680.5	n.77-32738T>C		intron_variant	Intron 1 of 6	3

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36672 AN: 151842 Hom.: 6200 Cov.: 31

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.0670

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.242 AC: 36765 AN: 151960 Hom.: 6237 Cov.: 31 AF XY: 0.247 AC XY: 18323 AN XY: 74302

African (AFR) AF: 0.443 AC: 18326 AN: 41374

American (AMR) AF: 0.344 AC: 5255 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3466

East Asian (EAS) AF: 0.256 AC: 1323 AN: 5164

South Asian (SAS) AF: 0.338 AC: 1629 AN: 4822

European-Finnish (FIN) AF: 0.137 AC: 1452 AN: 10582

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.114 AC: 7756 AN: 67984

Other (OTH) AF: 0.240 AC: 506 AN: 2110

Alfa AF: 0.150 Hom.: 3841

Bravo AF: 0.266

Asia WGS AF: 0.292 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.5
DANN	Benign	0.75
PhyloP100		0.49
Mutation Taster		=100/0	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: rs7313849; hg19: chr12-611594;