4-173208589-A-G

Variant names:

• chr4-173208589-A-G
• rs10213525
• NM_017423.3:c.127-39391A>G

Variant summary

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

The NM_017423.3(GALNT7):​c.127-39391A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,698 control chromosomes in the GnomAD database, including 15,289 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 0.44 (15289 hom., cov: 31)
• Consequence: GALNT7 NM_017423.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 4 publications found

Genes affected

GALNT7 (HGNC:4129): (polypeptide N-acetylgalactosaminyltransferase 7) This gene encodes GalNAc transferase 7, a member of the GalNAc-transferase family. The enzyme encoded by this gene controls the initiation step of mucin-type O-linked protein glycosylation and transfer of N-acetylgalactosamine to serine and threonine amino acid residues. This enzyme is a type II transmembrane protein and shares common sequence motifs with other family members. Unlike other family members, this enzyme shows exclusive specificity for partially GalNAc-glycosylated acceptor substrates and shows no activity with non-glycosylated peptides. This protein may function as a follow-up enzyme in the initiation step of O-glycosylation. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017423.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT7	NM_017423.3	MANE Select	c.127-39391A>G		intron	N/A	NP_059119.2
	GALNT7	NM_001375599.1		c.127-39391A>G		intron	N/A	NP_001362528.1
	GALNT7	NM_001375600.1		c.127-39391A>G		intron	N/A	NP_001362529.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT7	ENST00000265000.9	TSL:1 MANE Select	c.127-39391A>G		intron	N/A	ENSP00000265000.4
	GALNT7	ENST00000505308.6	TSL:2	c.127-39391A>G		intron	N/A	ENSP00000427095.2
	GALNT7	ENST00000857290.1		c.127-39391A>G		intron	N/A	ENSP00000527350.1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66090 AN: 151580 Hom.: 15278 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.436 AC: 66110 AN: 151698 Hom.: 15289 Cov.: 31 AF XY: 0.439 AC XY: 32549 AN XY: 74104

African (AFR) AF: 0.302 AC: 12467 AN: 41340

American (AMR) AF: 0.333 AC: 5071 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1738 AN: 3460

East Asian (EAS) AF: 0.668 AC: 3430 AN: 5138

South Asian (SAS) AF: 0.527 AC: 2523 AN: 4790

European-Finnish (FIN) AF: 0.548 AC: 5772 AN: 10526

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33469 AN: 67894

Other (OTH) AF: 0.450 AC: 946 AN: 2102

Alfa AF: 0.471 Hom.: 29781

Bravo AF: 0.413

Asia WGS AF: 0.540 AC: 1876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.44
PhyloP100		-0.074
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10213525; hg19: chr4-174129740;