NM_145649.5:c.925+44243T>C

Variant names:

• chr6-10574079-T-C
• rs1318748
• NM_145649.5:c.925+44243T>C

Variant summary

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

The NM_145649.5(GCNT2):​c.925+44243T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 152,104 control chromosomes in the GnomAD database, including 24,215 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 0.56 (24215 hom., cov: 33)
• Consequence: GCNT2 NM_145649.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

Genes affected

GCNT2 (HGNC:4204): (glucosaminyl (N-acetyl) transferase 2 (I blood group)) This gene encodes the enzyme responsible for formation of the blood group I antigen. The i and I antigens are distinguished by linear and branched poly-N-acetyllactosaminoglycans, respectively. The encoded protein is the I-branching enzyme, a beta-1,6-N-acetylglucosaminyltransferase responsible for the conversion of fetal i antigen to adult I antigen in erythrocytes during embryonic development. Mutations in this gene have been associated with adult i blood group phenotype. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GCNT2	NM_145649.5	c.925+44243T>C		intron_variant	Intron 3 of 4	ENST00000495262.7	NP_663624.1
GCNT2	NM_001491.3	c.919+16737T>C		intron_variant	Intron 1 of 2	ENST00000316170.9	NP_001482.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GCNT2	ENST00000495262.7	c.925+44243T>C		intron_variant	Intron 3 of 4	2	NM_145649.5	ENSP00000419411.2
GCNT2	ENST00000316170.9	c.919+16737T>C		intron_variant	Intron 1 of 2	1	NM_001491.3	ENSP00000314844.3

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85048 AN: 151986 Hom.: 24193 Cov.: 33

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.560 AC: 85104 AN: 152104 Hom.: 24215 Cov.: 33 AF XY: 0.562 AC XY: 41803 AN XY: 74322

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.594

Alfa AF: 0.579 Hom.: 14468

Bravo AF: 0.562

Asia WGS AF: 0.623 AC: 2166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1318748; hg19: chr6-10574312;