rs11167667

Variant names:

• chr5-154274385-C-T
• rs11167667
• NM_198321.4:c.160-20431C>T

Variant summary

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

The ENST00000297107.11(GALNT10):​c.160-20431C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,076 control chromosomes in the GnomAD database, including 12,085 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 0.36 (12085 hom., cov: 32)
• Consequence: GALNT10 ENST00000297107.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000297107.11. 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.160-20431C>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.160-20431C>T		intron	N/A	ENSP00000297107.6
	GALNT10	ENST00000377661.2	TSL:5	c.160-20431C>T		intron	N/A	ENSP00000366889.2
	GALNT10	ENST00000425427.6	TSL:2	c.160-20431C>T		intron	N/A	ENSP00000415210.2

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55311 AN: 151958 Hom.: 12067 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.364 AC: 55358 AN: 152076 Hom.: 12085 Cov.: 32 AF XY: 0.370 AC XY: 27516 AN XY: 74326

African (AFR) AF: 0.133 AC: 5520 AN: 41510

American (AMR) AF: 0.561 AC: 8574 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1564 AN: 3466

East Asian (EAS) AF: 0.762 AC: 3935 AN: 5164

South Asian (SAS) AF: 0.445 AC: 2144 AN: 4822

European-Finnish (FIN) AF: 0.394 AC: 4158 AN: 10546

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28223 AN: 67966

Other (OTH) AF: 0.393 AC: 829 AN: 2112

Alfa AF: 0.396 Hom.: 2345

Bravo AF: 0.372

Asia WGS AF: 0.563 AC: 1956 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.64
PhyloP100		-0.34
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: rs11167667; hg19: chr5-153653945;