rs2622694

chr3-138130027-C-T

Variant summary

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

The NM_016161.3(A4GNT):c.408+822G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 151,808 control chromosomes in the GnomAD database, including 31,036 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 0.64 (31036 hom., cov: 32)
• Consequence: A4GNT NM_016161.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434

Genes affected

A4GNT (HGNC:17968): (alpha-1,4-N-acetylglucosaminyltransferase) This gene encodes a protein from the glycosyltransferase 32 family. The enzyme catalyzes the transfer of N-acetylglucosamine (GlcNAc) to core 2 branched O-glycans. It forms a unique glycan, GlcNAcalpha1-->4Galbeta-->R and is largely associated with the Golgi apparatus membrane. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
A4GNT	NM_016161.3	c.408+822G>A		intron_variant		ENST00000236709.4
A4GNT	XM_017006543.3	c.408+822G>A		intron_variant
A4GNT	XM_017006544.2	c.408+822G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
A4GNT	ENST00000236709.4	c.408+822G>A		intron_variant		1	NM_016161.3	P1

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96734 AN: 151696 Hom.: 31012 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.638 AC: 96807 AN: 151808 Hom.: 31036 Cov.: 32 AF XY: 0.637 AC XY: 47247 AN XY: 74166

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.651

Alfa AF: 0.653 Hom.: 12428

Bravo AF: 0.639

Asia WGS AF: 0.556 AC: 1936 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	6.1
Dann	Benign	0.77

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: rs2622694; hg19: chr3-137848869;