chr3-138130027-C-T

Variant names:

• chr3-138130027-C-T
• rs2622694
• NM_016161.3:c.408+822G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
A4GNT	NM_016161.3	c.408+822G>A		intron_variant	Intron 2 of 2	ENST00000236709.4	NP_057245.1
A4GNT	XM_017006543.3	c.408+822G>A		intron_variant	Intron 2 of 2		XP_016862032.1
A4GNT	XM_017006544.2	c.408+822G>A		intron_variant	Intron 2 of 2		XP_016862033.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
A4GNT	ENST00000236709.4	c.408+822G>A		intron_variant	Intron 2 of 2	1	NM_016161.3	ENSP00000236709.3

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

African (AFR) AF: 0.578 AC: 23924 AN: 41396

American (AMR) AF: 0.690 AC: 10510 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2380 AN: 3468

East Asian (EAS) AF: 0.581 AC: 2996 AN: 5160

South Asian (SAS) AF: 0.596 AC: 2867 AN: 4810

European-Finnish (FIN) AF: 0.647 AC: 6769 AN: 10460

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45362 AN: 67964

Other (OTH) AF: 0.651 AC: 1371 AN: 2106

Alfa AF: 0.654 Hom.: 14125

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
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2622694; hg19: chr3-137848869;