rs10083335

Positions:

• chr14-69373392-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

GALNT16 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT16	XM_047431618.1	c.*3-12654C>T		intron_variant
GALNT16	XR_007064036.1	n.1813-6342C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.454

Alfa AF: 0.448 Hom.: 4799

Bravo AF: 0.437

Asia WGS AF: 0.362 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10083335; hg19: chr14-69840109;