rs725231

Variant names:

• chr2-153772722-A-C
• rs725231
• NM_001422879.1:c.-177+39892A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-153772722-A-C
• chr2-153772722-A-T

Variant summary

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

The NM_001422879.1(GALNT13):​c.-177+39892A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,086 control chromosomes in the GnomAD database, including 15,518 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 0.43 (15518 hom., cov: 32)
• Consequence: GALNT13 NM_001422879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 1 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT13	NM_001422879.1	c.-177+39892A>C		intron_variant	Intron 3 of 15		NP_001409808.1
GALNT13	NM_001422880.1	c.-177+39892A>C		intron_variant	Intron 3 of 14		NP_001409809.1
GALNT13	NM_001422881.1	c.-177+39892A>C		intron_variant	Intron 2 of 13		NP_001409810.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65446 AN: 151968 Hom.: 15493 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.431 AC: 65528 AN: 152086 Hom.: 15518 Cov.: 32 AF XY: 0.422 AC XY: 31382 AN XY: 74328

African (AFR) AF: 0.622 AC: 25779 AN: 41454

American (AMR) AF: 0.383 AC: 5849 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1263 AN: 3472

East Asian (EAS) AF: 0.0999 AC: 517 AN: 5174

South Asian (SAS) AF: 0.338 AC: 1631 AN: 4822

European-Finnish (FIN) AF: 0.331 AC: 3503 AN: 10582

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25773 AN: 67980

Other (OTH) AF: 0.384 AC: 809 AN: 2108

Alfa AF: 0.316 Hom.: 1165

Bravo AF: 0.440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.067
DANN	Benign	0.29
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs725231; hg19: chr2-154629235;