1-235448220-CA-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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]

TBCE Gene-Disease associations (from GenCC):

• hypoparathyroidism-retardation-dysmorphism syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Orphanet, G2P
• early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• encephalopathy, progressive, with amyotrophy and optic atrophy

  Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: PanelApp Australia, ClinGen, G2P, Ambry Genetics
• autosomal recessive Kenny-Caffey syndrome

  Inheritance: AR Classification: MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet

ENSG00000285053 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152490.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GALNT2	NM_152490.5	MANE Select	c.*1985delT		3_prime_UTR	Exon 12 of 12	NP_689703.1	Q8NCR0-1
	TBCE	NM_003193.5	MANE Select	c.1400-109delA		intron	N/A	NP_003184.1	Q15813-1
	TBCE	NM_001287801.2		c.1553-109delA		intron	N/A	NP_001274730.1	Q15813-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GALNT2	ENST00000366600.8	TSL:1 MANE Select	c.*1985delT		3_prime_UTR	Exon 12 of 12	ENSP00000355559.3	Q8NCR0-1
	TBCE	ENST00000642610.2	MANE Select	c.1400-109delA		intron	N/A	ENSP00000494796.1	Q15813-1
	ENSG00000285053	ENST00000647186.1		c.1400-109delA		intron	N/A	ENSP00000494775.1

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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.144 AC: 1538 AN: 10714

American (AMR) AF: 0.189 AC: 4299 AN: 22702

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 2512 AN: 14734

East Asian (EAS) AF: 0.234 AC: 6248 AN: 26686

South Asian (SAS) AF: 0.166 AC: 8063 AN: 48582

European-Finnish (FIN) AF: 0.203 AC: 5726 AN: 28274

Middle Eastern (MID) AF: 0.136 AC: 390 AN: 2870

European-Non Finnish (NFE) AF: 0.195 AC: 51227 AN: 262438

Other (OTH) AF: 0.200 AC: 4757 AN: 23836

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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

African (AFR) AF: 0.0828 AC: 1729 AN: 20874

American (AMR) AF: 0.0416 AC: 236 AN: 5672

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 80 AN: 1634

East Asian (EAS) AF: 0.0150 AC: 25 AN: 1664

South Asian (SAS) AF: 0.0341 AC: 54 AN: 1584

European-Finnish (FIN) AF: 0.0842 AC: 209 AN: 2482

Middle Eastern (MID) AF: 0.0397 AC: 5 AN: 126

European-Non Finnish (NFE) AF: 0.0535 AC: 1620 AN: 30294

Other (OTH) AF: 0.0494 AC: 43 AN: 870

Alfa AF: 0.00879 Hom.: 2

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-2.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs59405398; hg19: chr1-235611535;