7-7233928-G-T

Variant names:

• chr7-7233928-G-T
• rs1008898
• NM_020156.5:c.-17-375G>T

Variant summary

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

The NM_020156.5(C1GALT1):​c.-17-375G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,026 control chromosomes in the GnomAD database, including 7,261 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 0.29 (7261 hom., cov: 32)
• Consequence: C1GALT1 NM_020156.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 16 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1GALT1	NM_020156.5	c.-17-375G>T		intron_variant	Intron 1 of 3	ENST00000436587.7	NP_064541.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1GALT1	ENST00000436587.7	c.-17-375G>T		intron_variant	Intron 1 of 3	5	NM_020156.5	ENSP00000389176.2
C1GALT1	ENST00000476068.1	n.192-375G>T		intron_variant	Intron 1 of 1	1
C1GALT1	ENST00000429911.5	c.-17-375G>T		intron_variant	Intron 2 of 3	5		ENSP00000407666.1

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43364 AN: 151908 Hom.: 7249 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.286 AC: 43415 AN: 152026 Hom.: 7261 Cov.: 32 AF XY: 0.288 AC XY: 21396 AN XY: 74308

African (AFR) AF: 0.445 AC: 18458 AN: 41444

American (AMR) AF: 0.219 AC: 3348 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 540 AN: 3468

East Asian (EAS) AF: 0.528 AC: 2725 AN: 5162

South Asian (SAS) AF: 0.208 AC: 1002 AN: 4818

European-Finnish (FIN) AF: 0.267 AC: 2820 AN: 10560

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13760 AN: 67974

Other (OTH) AF: 0.261 AC: 552 AN: 2112

Alfa AF: 0.227 Hom.: 13203

Bravo AF: 0.292

Asia WGS AF: 0.352 AC: 1223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.46
PhyloP100		-0.064
PromoterAI		-0.0019	Neutral
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: rs1008898; hg19: chr7-7273559;