rs1546377

Variant names:

• chr3-16214870-C-G
• rs1546377
• NM_054110.5:c.1392+2107C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GALNT15	NM_054110.5	c.1392+2107C>G		intron_variant	Intron 6 of 9	ENST00000339732.10	NP_473451.3
GALNT15	NM_001319051.2	c.1392+2107C>G		intron_variant	Intron 6 of 9		NP_001305980.1
GALNT15	XM_005264852.6	c.1392+2107C>G		intron_variant	Intron 6 of 9		XP_005264909.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT15	ENST00000339732.10	c.1392+2107C>G		intron_variant	Intron 6 of 9	1	NM_054110.5	ENSP00000344260.5
GALNT15	ENST00000437509.3	c.1392+2107C>G		intron_variant	Intron 6 of 9	1		ENSP00000395873.1
GALNT15	ENST00000489467.1	n.66+2107C>G		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.755 AC: 31318 AN: 41466

American (AMR) AF: 0.739 AC: 11304 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2520 AN: 3468

East Asian (EAS) AF: 0.776 AC: 4020 AN: 5180

South Asian (SAS) AF: 0.792 AC: 3819 AN: 4820

European-Finnish (FIN) AF: 0.703 AC: 7433 AN: 10570

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45261 AN: 67978

Other (OTH) AF: 0.717 AC: 1515 AN: 2114

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
PhyloP100		-0.098
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: rs1546377; hg19: chr3-16256377;