5-154227372-C-T

Variant names:

• chr5-154227372-C-T
• rs2081015
• NM_198321.4:c.159+36347C>T

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+36347C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 151,920 control chromosomes in the GnomAD database, including 14,133 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 0.42 (14133 hom., cov: 32)
• Consequence: GALNT10 NM_198321.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668
• Publications: 8 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 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.159+36347C>T		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.159+36347C>T		intron	N/A	ENSP00000297107.6
	GALNT10	ENST00000377661.2	TSL:5	c.159+36347C>T		intron	N/A	ENSP00000366889.2
	GALNT10	ENST00000425427.6	TSL:2	c.159+36347C>T		intron	N/A	ENSP00000415210.2

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63487 AN: 151800 Hom.: 14118 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.418 AC: 63536 AN: 151920 Hom.: 14133 Cov.: 32 AF XY: 0.424 AC XY: 31478 AN XY: 74256

African (AFR) AF: 0.315 AC: 13060 AN: 41442

American (AMR) AF: 0.584 AC: 8895 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1557 AN: 3462

East Asian (EAS) AF: 0.838 AC: 4327 AN: 5166

South Asian (SAS) AF: 0.442 AC: 2127 AN: 4816

European-Finnish (FIN) AF: 0.394 AC: 4159 AN: 10558

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28088 AN: 67934

Other (OTH) AF: 0.437 AC: 919 AN: 2104

Alfa AF: 0.339 Hom.: 1345

Bravo AF: 0.434

Asia WGS AF: 0.584 AC: 2030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.23
PhyloP100		-0.67
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: rs2081015; hg19: chr5-153606932;