1-235448220-CAAAAAAAAAAAA-CAAAAAAAAAAA

Variant names:

• chr1-235448220-CA-C
• rs59405398
• NM_152490.5:c.*1985delT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_152490.5(B3GALNT2):​c.*1985delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 506,400 control chromosomes in the GnomAD database, including 46 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.062 (45 hom., cov: 24)
  • Exomes 𝑓: 0.19 (1 hom.)
• Consequence: B3GALNT2 NM_152490.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.40

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]

TBCE (HGNC:11582): (tubulin folding cofactor E) Cofactor E is one of four proteins (cofactors A, D, E, and C) involved in the pathway leading to correctly folded beta-tubulin from folding intermediates. Cofactors A and D are believed to play a role in capturing and stabilizing beta-tubulin intermediates in a quasi-native confirmation. Cofactor E binds to the cofactor D/beta-tubulin complex; interaction with cofactor C then causes the release of beta-tubulin polypeptides that are committed to the native state. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ENSG00000285053 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-235448220-CA-C is Benign according to our data. Variant chr1-235448220-CA-C is described in ClinVar as [Benign]. Clinvar id is 1242668.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GALNT2	NM_152490.5	c.*1985delT		3_prime_UTR_variant	Exon 12 of 12	ENST00000366600.8	NP_689703.1
TBCE	NM_003193.5	c.1400-109delA		intron_variant	Intron 15 of 16	ENST00000642610.2	NP_003184.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GALNT2	ENST00000366600	c.*1985delT		3_prime_UTR_variant	Exon 12 of 12	1	NM_152490.5	ENSP00000355559.3
TBCE	ENST00000642610.2	c.1400-109delA		intron_variant	Intron 15 of 16		NM_003193.5	ENSP00000494796.1
ENSG00000285053	ENST00000645655.1	c.1400-109delA		intron_variant	Intron 18 of 19			ENSP00000495202.1

Frequencies

GnomAD3 genomes AF: 0.0616 AC: 4038 AN: 65546 Hom.: 45 Cov.: 24

Gnomad AFR AF: 0.0829

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0417

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.0339

Gnomad FIN AF: 0.0842

Gnomad MID AF: 0.0362

Gnomad NFE AF: 0.0535

Gnomad OTH AF: 0.0500

GnomAD4 exome AF: 0.192 AC: 84760 AN: 440836 Hom.: 1 AF XY: 0.190 AC XY: 45393 AN XY: 238636

Gnomad4 AFR exome AF: 0.144

Gnomad4 AMR exome AF: 0.189

Gnomad4 ASJ exome AF: 0.170

Gnomad4 EAS exome AF: 0.234

Gnomad4 SAS exome AF: 0.166

Gnomad4 FIN exome AF: 0.203

Gnomad4 NFE exome AF: 0.195

Gnomad4 OTH exome AF: 0.200

GnomAD4 genome AF: 0.0616 AC: 4038 AN: 65564 Hom.: 45 Cov.: 24 AF XY: 0.0632 AC XY: 1932 AN XY: 30564

Gnomad4 AFR AF: 0.0828

Gnomad4 AMR AF: 0.0416

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.0150

Gnomad4 SAS AF: 0.0341

Gnomad4 FIN AF: 0.0842

Gnomad4 NFE AF: 0.0535

Gnomad4 OTH AF: 0.0494

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Oct 06, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs59405398; hg19: chr1-235611535;