rs2443527

Positions:

• chr5-154278152-A-G

Variant summary

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

The NM_198321.4(GALNT10):​c.160-16664A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.091 in 152,256 control chromosomes in the GnomAD database, including 741 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 0.091 (741 hom., cov: 32)
• Consequence: GALNT10 NM_198321.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT10	NM_198321.4	c.160-16664A>G		intron_variant		ENST00000297107.11	NP_938080.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT10	ENST00000297107.11	c.160-16664A>G		intron_variant		1	NM_198321.4	ENSP00000297107	P1

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13842 AN: 152138 Hom.: 741 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0841

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.0874

Gnomad SAS AF: 0.0739

Gnomad FIN AF: 0.0363

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.0971

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

GnomAD4 genome AF: 0.0910 AC: 13855 AN: 152256 Hom.: 741 Cov.: 32 AF XY: 0.0896 AC XY: 6670 AN XY: 74438

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0837

Gnomad4 ASJ AF: 0.0709

Gnomad4 EAS AF: 0.0874

Gnomad4 SAS AF: 0.0727

Gnomad4 FIN AF: 0.0363

Gnomad4 NFE AF: 0.0587

Gnomad4 OTH AF: 0.0966

Alfa AF: 0.0763 Hom.: 74

Bravo AF: 0.0968

Asia WGS AF: 0.0800 AC: 278 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.70

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: rs2443527; hg19: chr5-153657712;