rs10083335

Variant names:

• chr14-69373392-C-T
• rs10083335
• XM_047431618.1:c.*3-12654C>T

Variant summary

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

The XM_047431618.1(GALNT16):​c.*3-12654C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 152,084 control chromosomes in the GnomAD database, including 15,688 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 0.45 (15688 hom., cov: 32)
• Consequence: GALNT16 XM_047431618.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 0 publications found

Genes affected

GALNT16 (HGNC:23233): (polypeptide N-acetylgalactosaminyltransferase 16) Enables polypeptide N-acetylgalactosaminyltransferase activity. Involved in protein O-linked glycosylation via serine and protein O-linked glycosylation via threonine. Predicted to be located in Golgi membrane. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68620 AN: 151964 Hom.: 15673 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.452 AC: 68678 AN: 152084 Hom.: 15688 Cov.: 32 AF XY: 0.452 AC XY: 33607 AN XY: 74350

African (AFR) AF: 0.439 AC: 18214 AN: 41462

American (AMR) AF: 0.385 AC: 5888 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1915 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1295 AN: 5184

South Asian (SAS) AF: 0.491 AC: 2369 AN: 4824

European-Finnish (FIN) AF: 0.489 AC: 5163 AN: 10560

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.474 AC: 32224 AN: 67984

Other (OTH) AF: 0.454 AC: 959 AN: 2112

Alfa AF: 0.451 Hom.: 6042

Bravo AF: 0.437

Asia WGS AF: 0.362 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	14
DANN	Benign	0.53
PhyloP100		0.24

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10083335; hg19: chr14-69840109;