7-7182337-T-G

Variant names:

• chr7-7182337-T-G
• rs758263
• ENST00000429911.5:c.-18+24911T>G

Variant summary

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

The ENST00000429911.5(C1GALT1):​c.-18+24911T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,086 control chromosomes in the GnomAD database, including 21,121 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 0.51 (21121 hom., cov: 32)
• Consequence: C1GALT1 ENST00000429911.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 11 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429911.5. 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
	C1GALT1	NM_020156.5	MANE Select	c.-501T>G		upstream_gene	N/A	NP_064541.1	Q9NS00-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1GALT1	ENST00000429911.5	TSL:5	c.-18+24911T>G		intron	N/A	ENSP00000407666.1	C9K0C8
	C1GALT1	ENST00000436587.7	TSL:5 MANE Select	c.-501T>G		upstream_gene	N/A	ENSP00000389176.2	Q9NS00-1
	C1GALT1	ENST00000910742.1		c.-699T>G		upstream_gene	N/A	ENSP00000580801.1

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78226 AN: 151966 Hom.: 21091 Cov.: 32

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.375

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.515 AC: 78304 AN: 152086 Hom.: 21121 Cov.: 32 AF XY: 0.527 AC XY: 39168 AN XY: 74350

African (AFR) AF: 0.593 AC: 24576 AN: 41478

American (AMR) AF: 0.608 AC: 9289 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1237 AN: 3470

East Asian (EAS) AF: 0.923 AC: 4770 AN: 5170

South Asian (SAS) AF: 0.536 AC: 2586 AN: 4826

European-Finnish (FIN) AF: 0.511 AC: 5405 AN: 10586

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.425 AC: 28887 AN: 67956

Other (OTH) AF: 0.494 AC: 1042 AN: 2110

Alfa AF: 0.446 Hom.: 9264

Bravo AF: 0.528

Asia WGS AF: 0.724 AC: 2520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.39
DANN	Benign	0.55
PhyloP100		-1.5
PromoterAI		0.0088	Neutral

Splicing

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

Other links and lift over

dbSNP: rs758263; hg19: chr7-7221968;