rs12139970

chr1-230270714-G-T

Variant summary

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

The NM_004481.5(GALNT2):c.1441-3731G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,180 control chromosomes in the GnomAD database, including 3,969 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 0.20 (3969 hom., cov: 33)
• Consequence: GALNT2 NM_004481.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501

Genes affected

GALNT2 (HGNC:4124): (polypeptide N-acetylgalactosaminyltransferase 2) This gene encodes a member of the glycosyltransferase 2 protein family. Members of this family initiate mucin-type O-glycoslation of peptides in the Golgi apparatus. The encoded protein may be involved in O-linked glycosylation of the immunoglobulin A1 hinge region. This gene may influence triglyceride levels, and may be involved Type 2 diabetes, as well as several types of cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT2	NM_004481.5	c.1441-3731G>T		intron_variant		ENST00000366672.5
LOC124904542	XR_007066928.1	n.441+956C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT2	ENST00000366672.5	c.1441-3731G>T		intron_variant		1	NM_004481.5	P1
	ENST00000440729.2	n.431+956C>A		intron_variant, non_coding_transcript_variant		3
GALNT2	ENST00000485438.1	n.1093-3731G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30877 AN: 152062 Hom.: 3966 Cov.: 33

Gnomad AFR AF: 0.0491

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.0431

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.203 AC: 30891 AN: 152180 Hom.: 3969 Cov.: 33 AF XY: 0.205 AC XY: 15232 AN XY: 74398

Gnomad4 AFR AF: 0.0490

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.0432

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.223

Alfa AF: 0.267 Hom.: 5307

Bravo AF: 0.188

Asia WGS AF: 0.168 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	7.3
Dann	Benign	0.83

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: rs12139970; hg19: chr1-230406460;