rs1546377

Positions:

• chr3-16214870-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_054110.5(GALNT15):​c.1392+2107C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,102 control chromosomes in the GnomAD database, including 38,564 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 0.71 (38564 hom., cov: 31)
• Consequence: GALNT15 NM_054110.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

Genes affected

GALNT15 (HGNC:21531): (polypeptide N-acetylgalactosaminyltransferase 15) Predicted to enable polypeptide N-acetylgalactosaminyltransferase activity. Predicted to be involved in O-glycan processing. Located in transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]

GALNT15 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT15	NM_054110.5	c.1392+2107C>G		intron_variant		ENST00000339732.10	NP_473451.3
GALNT15	NM_001319051.2	c.1392+2107C>G		intron_variant			NP_001305980.1
GALNT15	XM_005264852.6	c.1392+2107C>G		intron_variant			XP_005264909.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT15	ENST00000339732.10	c.1392+2107C>G		intron_variant		1	NM_054110.5	ENSP00000344260.5
GALNT15	ENST00000437509.3	c.1392+2107C>G		intron_variant		1		ENSP00000395873.1
GALNT15	ENST00000489467.1	n.66+2107C>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107863 AN: 151984 Hom.: 38527 Cov.: 31

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.710 AC: 107958 AN: 152102 Hom.: 38564 Cov.: 31 AF XY: 0.714 AC XY: 53075 AN XY: 74364

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.792

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.717

Alfa AF: 0.688 Hom.: 4505

Bravo AF: 0.717

Asia WGS AF: 0.764 AC: 2654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.53

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

Publications

LitVar

Other links and lift over

dbSNP: rs1546377; hg19: chr3-16256377;