rs1468995

Variant names:

• chr2-154160912-C-A
• rs1468995
• NM_052917.4:c.311+20407C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-154160912-C-A
• chr2-154160912-C-T

Variant summary

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

The NM_052917.4(GALNT13):​c.311+20407C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,204 control chromosomes in the GnomAD database, including 3,330 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 0.18 (3330 hom., cov: 32)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 3 publications found

Genes affected

GALNT13 (HGNC:23242): (polypeptide N-acetylgalactosaminyltransferase 13) The GALNT13 protein is a member of the UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase (GalNAcT; EC 2.4.1.41) family, which initiate O-linked glycosylation of mucins (see MUC3A, MIM 158371) by the initial transfer of N-acetylgalactosamine (GalNAc) with an alpha-linkage to a serine or threonine residue.[supplied by OMIM, Apr 2004]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT13	NM_052917.4	c.311+20407C>A		intron_variant	Intron 4 of 12	ENST00000392825.8	NP_443149.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT13	ENST00000392825.8	c.311+20407C>A		intron_variant	Intron 4 of 12	2	NM_052917.4	ENSP00000376570.3
GALNT13	ENST00000409237.5	c.311+20407C>A		intron_variant	Intron 2 of 11	1		ENSP00000387239.1
GALNT13	ENST00000431076.5	n.164+20407C>A		intron_variant	Intron 1 of 8	1		ENSP00000389447.1

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27781 AN: 152086 Hom.: 3329 Cov.: 32

Gnomad AFR AF: 0.0479

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.183 AC: 27781 AN: 152204 Hom.: 3330 Cov.: 32 AF XY: 0.179 AC XY: 13344 AN XY: 74402

African (AFR) AF: 0.0478 AC: 1985 AN: 41556

American (AMR) AF: 0.189 AC: 2883 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 961 AN: 3472

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5182

South Asian (SAS) AF: 0.122 AC: 588 AN: 4824

European-Finnish (FIN) AF: 0.278 AC: 2935 AN: 10570

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17847 AN: 67996

Other (OTH) AF: 0.153 AC: 324 AN: 2114

Alfa AF: 0.156 Hom.: 451

Bravo AF: 0.168

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.67
PhyloP100		0.082
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: rs1468995; hg19: chr2-155017425;