rs1047763

chr7-7243938-G-A

Variant summary

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

The NM_020156.5(C1GALT1):c.*211G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 344,742 control chromosomes in the GnomAD database, including 8,889 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 0.22 (4184 hom., cov: 32)
  • Exomes 𝑓: 0.18 (4705 hom.)
• Consequence: C1GALT1 NM_020156.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1GALT1	NM_020156.5	c.*211G>A		3_prime_UTR_variant	4/4	ENST00000436587.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1GALT1	ENST00000436587.7	c.*211G>A		3_prime_UTR_variant	4/4	5	NM_020156.5	P1
C1GALT1	ENST00000223122.4	c.*211G>A		3_prime_UTR_variant	3/3	1		P1

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33563 AN: 151772 Hom.: 4174 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.207

GnomAD4 exome AF: 0.184 AC: 35496 AN: 192852 Hom.: 4705 Cov.: 3 AF XY: 0.181 AC XY: 17913 AN XY: 99128

Gnomad4 AFR exome AF: 0.247

Gnomad4 AMR exome AF: 0.209

Gnomad4 ASJ exome AF: 0.127

Gnomad4 EAS exome AF: 0.576

Gnomad4 SAS exome AF: 0.0740

Gnomad4 FIN exome AF: 0.215

Gnomad4 NFE exome AF: 0.146

Gnomad4 OTH exome AF: 0.173

GnomAD4 genome AF: 0.221 AC: 33590 AN: 151890 Hom.: 4184 Cov.: 32 AF XY: 0.226 AC XY: 16799 AN XY: 74238

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.207

Alfa AF: 0.182 Hom.: 2549

Bravo AF: 0.222

Asia WGS AF: 0.309 AC: 1073 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.6
Dann	Benign	0.75
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs1047763; hg19: chr7-7283569;