rs2166488

chr2-157303324-A-Gchr2-157303324-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT5	NM_014568.3	c.2439+2325A>G		intron_variant		ENST00000259056.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT5	ENST00000259056.5	c.2439+2325A>G		intron_variant		1	NM_014568.3	P1

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

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.922

Gnomad4 OTH AF: 0.767

Alfa AF: 0.834 Hom.: 24580

Bravo AF: 0.700

Asia WGS AF: 0.846 AC: 2935 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.2
Dann	Benign	0.44

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: rs2166488; hg19: chr2-158159836;