rs12523441

Variant names:

• chr5-154275107-C-T
• rs12523441
• NM_198321.4:c.160-19709C>T

Variant summary

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

The NM_198321.4(GALNT10):​c.160-19709C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,166 control chromosomes in the GnomAD database, including 12,098 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 0.36 (12098 hom., cov: 33)
• Consequence: GALNT10 NM_198321.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 4 publications found

Genes affected

GALNT10 (HGNC:19873): (polypeptide N-acetylgalactosaminyltransferase 10) This gene encodes a member of the GalNAc polypeptide N-acetylgalactosaminyltransferases. These enzymes catalyze the first step in the synthesis of mucin-type oligosaccharides. These proteins transfer GalNAc from UDP-GalNAc to either serine or threonine residues of polypeptide acceptors. The protein encoded by this locus may have increased catalytic activity toward glycosylated peptides compared to activity toward non-glycosylated peptides.[provided by RefSeq, Apr 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT10	NM_198321.4	c.160-19709C>T		intron_variant	Intron 1 of 11	ENST00000297107.11	NP_938080.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT10	ENST00000297107.11	c.160-19709C>T		intron_variant	Intron 1 of 11	1	NM_198321.4	ENSP00000297107.6

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55354 AN: 152048 Hom.: 12080 Cov.: 33

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.364 AC: 55401 AN: 152166 Hom.: 12098 Cov.: 33 AF XY: 0.370 AC XY: 27553 AN XY: 74394

African (AFR) AF: 0.133 AC: 5531 AN: 41528

American (AMR) AF: 0.561 AC: 8578 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1568 AN: 3472

East Asian (EAS) AF: 0.762 AC: 3942 AN: 5174

South Asian (SAS) AF: 0.444 AC: 2143 AN: 4826

European-Finnish (FIN) AF: 0.394 AC: 4166 AN: 10564

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28233 AN: 67994

Other (OTH) AF: 0.393 AC: 829 AN: 2110

Alfa AF: 0.411 Hom.: 10146

Bravo AF: 0.372

Asia WGS AF: 0.563 AC: 1957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.58
PhyloP100		-0.18
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: rs12523441; hg19: chr5-153654667;