NM_020156.5:c.889-606A>G

Variant names:

• chr7-7242918-A-G
• rs7790522
• NM_020156.5:c.889-606A>G

Variant summary

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

The NM_020156.5(C1GALT1):​c.889-606A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,940 control chromosomes in the GnomAD database, including 7,770 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 0.30 (7770 hom., cov: 32)
• Consequence: C1GALT1 NM_020156.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 6 publications found

Genes affected

C1GALT1 (HGNC:24337): (core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1) The protein encoded by this gene generates the common core 1 O-glycan structure, Gal-beta-1-3GalNAc-R, by the transfer of Gal from UDP-Gal to GalNAc-alpha-1-R. Core 1 is a precursor for many extended mucin-type O-glycans on cell surface and secreted glycoproteins. Studies in mice suggest that this gene plays a key role in thrombopoiesis and kidney homeostasis.[provided by RefSeq, Sep 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020156.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1GALT1	NM_020156.5	MANE Select	c.889-606A>G		intron	N/A	NP_064541.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1GALT1	ENST00000436587.7	TSL:5 MANE Select	c.889-606A>G		intron	N/A	ENSP00000389176.2
	C1GALT1	ENST00000223122.4	TSL:1	c.889-606A>G		intron	N/A	ENSP00000223122.2

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46125 AN: 151822 Hom.: 7759 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.304 AC: 46159 AN: 151940 Hom.: 7770 Cov.: 32 AF XY: 0.311 AC XY: 23069 AN XY: 74282

African (AFR) AF: 0.366 AC: 15187 AN: 41454

American (AMR) AF: 0.266 AC: 4059 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 787 AN: 3466

East Asian (EAS) AF: 0.714 AC: 3694 AN: 5174

South Asian (SAS) AF: 0.263 AC: 1269 AN: 4818

European-Finnish (FIN) AF: 0.352 AC: 3722 AN: 10562

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16448 AN: 67872

Other (OTH) AF: 0.291 AC: 612 AN: 2106

Alfa AF: 0.283 Hom.: 815

Bravo AF: 0.304

Asia WGS AF: 0.468 AC: 1624 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.48
DANN	Benign	0.65
PhyloP100		-1.2
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: rs7790522; hg19: chr7-7282549;