rs10875583

Variant names:

• chr5-154234156-G-C
• rs10875583
• NM_198321.4:c.159+43131G>C

Variant summary

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

The NM_198321.4(GALNT10):​c.159+43131G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 152,124 control chromosomes in the GnomAD database, including 12,375 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 0.37 (12375 hom., cov: 32)
• Consequence: GALNT10 NM_198321.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT10	NM_198321.4	c.159+43131G>C		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.159+43131G>C		intron_variant	Intron 1 of 11	1	NM_198321.4	ENSP00000297107.6

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55834 AN: 152006 Hom.: 12365 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.367 AC: 55853 AN: 152124 Hom.: 12375 Cov.: 32 AF XY: 0.374 AC XY: 27797 AN XY: 74342

African (AFR) AF: 0.134 AC: 5581 AN: 41520

American (AMR) AF: 0.560 AC: 8562 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1556 AN: 3464

East Asian (EAS) AF: 0.830 AC: 4298 AN: 5178

South Asian (SAS) AF: 0.442 AC: 2135 AN: 4826

European-Finnish (FIN) AF: 0.398 AC: 4203 AN: 10560

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28278 AN: 67978

Other (OTH) AF: 0.393 AC: 831 AN: 2112

Alfa AF: 0.383 Hom.: 1559

Bravo AF: 0.375

Asia WGS AF: 0.576 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.0
DANN	Benign	0.73
PhyloP100		-0.51
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: rs10875583; hg19: chr5-153613716;