7-7182337-T-G

Position:

• chr7-7182337-T-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1GALT1	XM_047420620.1	c.-216+24911T>G		intron_variant
C1GALT1	XM_047420623.1	c.-18+24911T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1GALT1	ENST00000429911.5	c.-18+24911T>G		intron_variant		5

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

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.494

Alfa AF: 0.447 Hom.: 8532

Bravo AF: 0.528

Asia WGS AF: 0.724 AC: 2520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.39
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs758263; hg19: chr7-7221968;