12-502428-T-C

Position:

• chr12-502428-T-C

Variant summary

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

The ENST00000266383.10(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 ENST00000266383.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
B4GALNT3	NM_173593.4	c.170-32738T>C		intron_variant		ENST00000266383.10	NP_775864.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
B4GALNT3	ENST00000266383.10	c.170-32738T>C		intron_variant		1	NM_173593.4	ENSP00000266383	P1
B4GALNT3	ENST00000535680.5	n.77-32738T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.240

Alfa AF: 0.147 Hom.: 3120

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

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: rs7313849; hg19: chr12-611594;