rs42935

Positions:

• chr22-30566755-A-G

Variant summary

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

The NM_001318104.2(GAL3ST1):​c.-120+7711T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,470 control chromosomes in the GnomAD database, including 14,085 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 0.43 (14085 hom., cov: 30)
• Consequence: GAL3ST1 NM_001318104.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

Genes affected

GAL3ST1 (HGNC:24240): (galactose-3-O-sulfotransferase 1) Sulfonation, an important step in the metabolism of many drugs, xenobiotics, hormones, and neurotransmitters, is catalyzed by sulfotransferases. This gene encodes galactosylceramide sulfotransferase, which catalyzes the sulfation of membrane glycolipids including the final step in the synthesis of sulfatide, a major lipid component of the myelin sheath. This gene exhibits elevated expression in ovarian epithelial carcinoma and the encoded enzyme exhibits elevated activity in renal cell carcinoma. Mutations in this gene may be associated with reduced insulin resistance. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAL3ST1	NM_001318104.2	c.-120+7711T>C		intron_variant		ENST00000406361.6	NP_001305033.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAL3ST1	ENST00000406361.6	c.-120+7711T>C		intron_variant		2	NM_001318104.2	ENSP00000385207.1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 64981 AN: 151352 Hom.: 14056 Cov.: 30

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.430 AC: 65058 AN: 151470 Hom.: 14085 Cov.: 30 AF XY: 0.432 AC XY: 31936 AN XY: 73982

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.413

Alfa AF: 0.428 Hom.: 1702

Bravo AF: 0.422

Asia WGS AF: 0.408 AC: 1421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.68
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs42935; hg19: chr22-30962742;