1-235489208-C-T

Variant names:

• chr1-235489208-C-T
• rs291396
• NM_152490.5:c.321G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4 BP6_Moderate BP7 BA1

The NM_152490.5(B3GALNT2):​c.321G>A​(p.Glu107Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 1,613,652 control chromosomes in the GnomAD database, including 184,357 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.45 (16000 hom., cov: 32)
  • Exomes 𝑓: 0.47 (168357 hom.)
• Consequence: B3GALNT2 NM_152490.5 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.249

Genes affected

B3GALNT2 (HGNC:28596): (beta-1,3-N-acetylgalactosaminyltransferase 2) This gene encodes a member of the glycosyltransferase 31 family. The encoded protein synthesizes GalNAc:beta-1,3GlcNAc, a novel carbohydrate structure, on N- and O-glycans. Alternatively spliced transcript variants that encode different isoforms have been described. [provided by RefSeq, Mar 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.09).
• BP6: Variant 1-235489208-C-T is Benign according to our data. Variant chr1-235489208-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 473884.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.249 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GALNT2	NM_152490.5	c.321G>A	p.Glu107Glu	synonymous_variant	Exon 3 of 12	ENST00000366600.8	NP_689703.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GALNT2	ENST00000366600.8	c.321G>A	p.Glu107Glu	synonymous_variant	Exon 3 of 12	1	NM_152490.5	ENSP00000355559.3

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68251 AN: 151900 Hom.: 15986 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.479

GnomAD4 exome AF: 0.471 AC: 688384 AN: 1461632 Hom.: 168357 Cov.: 62 AF XY: 0.467 AC XY: 339453 AN XY: 727102

Gnomad4 AFR exome AF: 0.428

Gnomad4 AMR exome AF: 0.255

Gnomad4 ASJ exome AF: 0.490

Gnomad4 EAS exome AF: 0.131

Gnomad4 SAS exome AF: 0.280

Gnomad4 FIN exome AF: 0.524

Gnomad4 NFE exome AF: 0.506

Gnomad4 OTH exome AF: 0.450

GnomAD4 genome AF: 0.449 AC: 68292 AN: 152020 Hom.: 16000 Cov.: 32 AF XY: 0.442 AC XY: 32852 AN XY: 74282

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.480

Alfa AF: 0.487 Hom.: 23632

Bravo AF: 0.436

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.090
CADD	Benign	5.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs291396; hg19: chr1-235652513;