2-157260788-C-T

Variant summary

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

The NM_014568.3(GALNT5):c.1454+1252C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,092 control chromosomes in the GnomAD database, including 5,782 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 0.23 (5782 hom., cov: 32)
• Consequence: GALNT5 NM_014568.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT5	NM_014568.3	c.1454+1252C>T		intron_variant		ENST00000259056.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT5	ENST00000259056.5	c.1454+1252C>T		intron_variant		1	NM_014568.3	P1

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34285 AN: 151974 Hom.: 5759 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.226 AC: 34349 AN: 152092 Hom.: 5782 Cov.: 32 AF XY: 0.224 AC XY: 16626 AN XY: 74342

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.0789

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.204

Alfa AF: 0.127 Hom.: 702

Bravo AF: 0.238

Asia WGS AF: 0.127 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.1
Dann	Benign	0.56

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: rs16841426; hg19: chr2-158117300;