rs153431

Positions:

• chr5-154269366-T-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
GALNT10	NM_198321.4	c.160-25450T>A		intron_variant		ENST00000297107.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT10	ENST00000297107.11	c.160-25450T>A		intron_variant		1	NM_198321.4	P1

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

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0991

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.217

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

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: rs153431; hg19: chr5-153648926; COSMIC: COSV51723193;