chr5-154308540-G-A

Variant names:

• chr5-154308540-G-A
• rs6890748
• NM_198321.4:c.401+10461G>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.401+10461G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 152,110 control chromosomes in the GnomAD database, including 12,585 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 0.40 (12585 hom., cov: 32)
• Consequence: GALNT10 NM_198321.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198321.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT10	NM_198321.4	MANE Select	c.401+10461G>A		intron	N/A	NP_938080.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT10	ENST00000297107.11	TSL:1 MANE Select	c.401+10461G>A		intron	N/A	ENSP00000297107.6
	GALNT10	ENST00000377661.2	TSL:5	c.401+10461G>A		intron	N/A	ENSP00000366889.2
	GALNT10	ENST00000425427.6	TSL:2	c.401+10461G>A		intron	N/A	ENSP00000415210.2

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60696 AN: 151990 Hom.: 12581 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.0487

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.399 AC: 60725 AN: 152110 Hom.: 12585 Cov.: 32 AF XY: 0.393 AC XY: 29252 AN XY: 74356

African (AFR) AF: 0.425 AC: 17643 AN: 41474

American (AMR) AF: 0.303 AC: 4623 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1484 AN: 3472

East Asian (EAS) AF: 0.0488 AC: 253 AN: 5182

South Asian (SAS) AF: 0.292 AC: 1408 AN: 4822

European-Finnish (FIN) AF: 0.440 AC: 4652 AN: 10576

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.430 AC: 29232 AN: 67988

Other (OTH) AF: 0.390 AC: 823 AN: 2110

Alfa AF: 0.406 Hom.: 2455

Bravo AF: 0.388

Asia WGS AF: 0.199 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.57
PhyloP100		0.015
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: rs6890748; hg19: chr5-153688100;