rs153431

Variant names:

• chr5-154269366-T-A
• rs153431
• NM_198321.4:c.160-25450T>A

Variant summary

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

The NM_198321.4(GALNT10):​c.160-25450T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,054 control chromosomes in the GnomAD database, including 5,514 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 0.24 (5514 hom., cov: 31)
• Consequence: GALNT10 NM_198321.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT10	NM_198321.4	c.160-25450T>A		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.160-25450T>A		intron_variant	Intron 1 of 11	1	NM_198321.4	ENSP00000297107.6

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37080 AN: 151936 Hom.: 5498 Cov.: 31

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0990

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.244 AC: 37134 AN: 152054 Hom.: 5514 Cov.: 31 AF XY: 0.242 AC XY: 17972 AN XY: 74326

African (AFR) AF: 0.422 AC: 17465 AN: 41424

American (AMR) AF: 0.130 AC: 1991 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 441 AN: 3470

East Asian (EAS) AF: 0.0991 AC: 513 AN: 5178

South Asian (SAS) AF: 0.169 AC: 813 AN: 4822

European-Finnish (FIN) AF: 0.225 AC: 2377 AN: 10572

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12720 AN: 67980

Other (OTH) AF: 0.217 AC: 459 AN: 2112

Alfa AF: 0.219 Hom.: 536

Bravo AF: 0.246

Asia WGS AF: 0.145 AC: 506 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	0.063
DANN	Benign	0.50
PhyloP100		-0.78
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: rs153431; hg19: chr5-153648926; COSMIC: COSV51723193;