chr2-157303324-A-G

Variant names:

• chr2-157303324-A-G
• rs2166488
• NM_014568.3:c.2439+2325A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014568.3(GALNT5):​c.2439+2325A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 152,112 control chromosomes in the GnomAD database, including 45,824 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 0.73 (45824 hom., cov: 33)
• Consequence: GALNT5 NM_014568.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191
• Publications: 2 publications found

Genes affected

GALNT5 (HGNC:4127): (polypeptide N-acetylgalactosaminyltransferase 5) The protein encoded by this gene is a membrane-bound polypeptide N-acetylgalactosaminyltransferase that is found in the Golgi. The encoded protein catalyzes the first step in the mucin-type O-glycosylation of Golgi proteins, transfering an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. [provided by RefSeq, Aug 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014568.3. 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
	GALNT5	NM_014568.3	MANE Select	c.2439+2325A>G		intron	N/A	NP_055383.1
	GALNT5	NM_001329868.2		c.1029+2325A>G		intron	N/A	NP_001316797.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT5	ENST00000259056.5	TSL:1 MANE Select	c.2439+2325A>G		intron	N/A	ENSP00000259056.4
	GALNT5	ENST00000953167.1		c.2439+2325A>G		intron	N/A	ENSP00000623226.1
	GALNT5	ENST00000953166.1		c.2418+2325A>G		intron	N/A	ENSP00000623225.1

Frequencies

GnomAD3 genomes AF: 0.730 AC: 111014 AN: 151994 Hom.: 45835 Cov.: 33

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.730 AC: 111009 AN: 152112 Hom.: 45824 Cov.: 33 AF XY: 0.732 AC XY: 54408 AN XY: 74342

African (AFR) AF: 0.314 AC: 13033 AN: 41498

American (AMR) AF: 0.773 AC: 11807 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3171 AN: 3468

East Asian (EAS) AF: 0.823 AC: 4257 AN: 5174

South Asian (SAS) AF: 0.909 AC: 4389 AN: 4828

European-Finnish (FIN) AF: 0.847 AC: 8959 AN: 10574

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.922 AC: 62648 AN: 67976

Other (OTH) AF: 0.767 AC: 1623 AN: 2116

Alfa AF: 0.832 Hom.: 36687

Bravo AF: 0.700

Asia WGS AF: 0.846 AC: 2935 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.2
DANN	Benign	0.44
PhyloP100		0.19
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: rs2166488; hg19: chr2-158159836;