7-7228800-C-T

Variant summary

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

The NM_020156.5(C1GALT1):c.-17-5503C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 152,020 control chromosomes in the GnomAD database, including 24,494 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 0.55 (24494 hom., cov: 31)
• Consequence: C1GALT1 NM_020156.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1GALT1	NM_020156.5	c.-17-5503C>T		intron_variant		ENST00000436587.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1GALT1	ENST00000436587.7	c.-17-5503C>T		intron_variant		5	NM_020156.5	P1
C1GALT1	ENST00000476068.1	n.192-5503C>T		intron_variant, non_coding_transcript_variant		1
C1GALT1	ENST00000429911.5	c.-17-5503C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82921 AN: 151902 Hom.: 24465 Cov.: 31

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.546 AC: 82993 AN: 152020 Hom.: 24494 Cov.: 31 AF XY: 0.541 AC XY: 40197 AN XY: 74322

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.557

Alfa AF: 0.460 Hom.: 37353

Bravo AF: 0.561

Asia WGS AF: 0.522 AC: 1814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	4.6
Dann	Benign	0.57

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: rs10259085; hg19: chr7-7268431;