rs10083154

chr12-57627150-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001478.5(B4GALNT1):c.1385-189C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,874 control chromosomes in the GnomAD database, including 11,168 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.37 (11168 hom., cov: 31)
• Consequence: B4GALNT1 NM_001478.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.149

Genes affected

B4GALNT1 (HGNC:4117): (beta-1,4-N-acetyl-galactosaminyltransferase 1) GM2 and GD2 gangliosides are sialic acid-containing glycosphingolipids. GalNAc-T is the enzyme involved in the biosynthesis of G(M2) and G(D2) glycosphingolipids. GalNAc-T catalyzes the transfer of GalNAc into G(M3) and G(D3) by a beta-1,4 linkage, resulting in the synthesis of G(M2) and G(D2), respectively. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2013]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 12-57627150-G-A is Benign according to our data. Variant chr12-57627150-G-A is described in ClinVar as [Benign]. Clinvar id is 1266146.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
B4GALNT1	NM_001478.5	c.1385-189C>T		intron_variant		ENST00000341156.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B4GALNT1	ENST00000341156.9	c.1385-189C>T		intron_variant		1	NM_001478.5	P1

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56863 AN: 151756 Hom.: 11149 Cov.: 31

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.375 AC: 56922 AN: 151874 Hom.: 11168 Cov.: 31 AF XY: 0.383 AC XY: 28394 AN XY: 74224

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.336

Alfa AF: 0.348 Hom.: 4783

Bravo AF: 0.372

Asia WGS AF: 0.559 AC: 1942 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 29, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.3
Dann	Benign	0.74

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: rs10083154; hg19: chr12-58020933;