NM_020156.5:c.*211G>A

Variant names:

• chr7-7243938-G-A
• rs1047763
• NM_020156.5:c.*211G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 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.*211G>A		3_prime_UTR	Exon 4 of 4	NP_064541.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1GALT1	ENST00000436587.7	TSL:5 MANE Select	c.*211G>A		3_prime_UTR	Exon 4 of 4	ENSP00000389176.2
	C1GALT1	ENST00000223122.4	TSL:1	c.*211G>A		3_prime_UTR	Exon 3 of 3	ENSP00000223122.2

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

African (AFR) AF: 0.247 AC: 1397 AN: 5662

American (AMR) AF: 0.209 AC: 1482 AN: 7096

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 959 AN: 7542

East Asian (EAS) AF: 0.576 AC: 8016 AN: 13926

South Asian (SAS) AF: 0.0740 AC: 682 AN: 9220

European-Finnish (FIN) AF: 0.215 AC: 2353 AN: 10938

Middle Eastern (MID) AF: 0.146 AC: 145 AN: 994

European-Non Finnish (NFE) AF: 0.146 AC: 18238 AN: 124604

Other (OTH) AF: 0.173 AC: 2224 AN: 12870

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

African (AFR) AF: 0.267 AC: 11071 AN: 41432

American (AMR) AF: 0.209 AC: 3189 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3472

East Asian (EAS) AF: 0.542 AC: 2803 AN: 5176

South Asian (SAS) AF: 0.117 AC: 564 AN: 4824

European-Finnish (FIN) AF: 0.280 AC: 2944 AN: 10532

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11751 AN: 67882

Other (OTH) AF: 0.207 AC: 435 AN: 2102

Alfa AF: 0.193 Hom.: 4559

Bravo AF: 0.222

Asia WGS AF: 0.309 AC: 1073 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.75
PhyloP100		-0.28
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs1047763; hg19: chr7-7283569;