rs1125078

Variant names:

• chr11-66042404-C-A
• rs1125078
• NM_033036.3:c.*103G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-66042404-C-A
• chr11-66042404-C-T
• chr11-66042404-C-G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_033036.3(GAL3ST3):​c.*103G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 897,920 control chromosomes in the GnomAD database, including 309,616 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.76 (45031 hom., cov: 32)
  • Exomes 𝑓: 0.84 (264585 hom.)
• Consequence: GAL3ST3 NM_033036.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.36
• Publications: 10 publications found

Genes affected

GAL3ST3 (HGNC:24144): (galactose-3-O-sulfotransferase 3) This gene encodes a member of the galactose-3-O-sulfotransferase protein family. The product of this gene catalyzes sulfonation by transferring a sulfate group to the 3' position of galactose in N-acetyllactosamine in both type 2 (Gal-beta-1-4GlcNAc-R) oligosaccharides and core-2-branched O-glycans, but not on type 1 or core-1-branched structures. This gene, which has also been referred to as GAL3ST2, is different from the GAL3ST2 gene located on chromosome 2 that encodes a related enzyme with distinct tissue distribution and substrate specificities, compared to galactose-3-O-sulfotransferase 3. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 11-66042404-C-A is Benign according to our data. Variant chr11-66042404-C-A is described in ClinVar as Benign. ClinVar VariationId is 1223944.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033036.3. 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
	GAL3ST3	NM_033036.3	MANE Select	c.*103G>T		3_prime_UTR	Exon 3 of 3	NP_149025.1	Q96A11

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAL3ST3	ENST00000312006.5	TSL:1 MANE Select	c.*103G>T		3_prime_UTR	Exon 3 of 3	ENSP00000308591.3	Q96A11
	GAL3ST3	ENST00000527878.1	TSL:1	c.*103G>T		3_prime_UTR	Exon 2 of 2	ENSP00000434829.1	Q96A11
	GAL3ST3	ENST00000882250.1		c.*103G>T		3_prime_UTR	Exon 3 of 3	ENSP00000552309.1

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115409 AN: 151964 Hom.: 45000 Cov.: 32

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.903

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.756

GnomAD4 exome AF: 0.841 AC: 626921 AN: 745838 Hom.: 264585 Cov.: 10 AF XY: 0.840 AC XY: 313155 AN XY: 372650

African (AFR) AF: 0.563 AC: 8530 AN: 15148

American (AMR) AF: 0.856 AC: 11221 AN: 13110

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 12168 AN: 14610

East Asian (EAS) AF: 0.809 AC: 22248 AN: 27484

South Asian (SAS) AF: 0.831 AC: 38393 AN: 46194

European-Finnish (FIN) AF: 0.846 AC: 25152 AN: 29724

Middle Eastern (MID) AF: 0.773 AC: 1962 AN: 2538

European-Non Finnish (NFE) AF: 0.851 AC: 478150 AN: 561622

Other (OTH) AF: 0.822 AC: 29097 AN: 35408

GnomAD4 genome AF: 0.759 AC: 115487 AN: 152082 Hom.: 45031 Cov.: 32 AF XY: 0.762 AC XY: 56675 AN XY: 74346

African (AFR) AF: 0.569 AC: 23623 AN: 41486

American (AMR) AF: 0.812 AC: 12421 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2847 AN: 3472

East Asian (EAS) AF: 0.777 AC: 3982 AN: 5122

South Asian (SAS) AF: 0.820 AC: 3957 AN: 4828

European-Finnish (FIN) AF: 0.847 AC: 8974 AN: 10598

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57061 AN: 67972

Other (OTH) AF: 0.753 AC: 1589 AN: 2110

Alfa AF: 0.783 Hom.: 7547

Bravo AF: 0.749

Asia WGS AF: 0.770 AC: 2676 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.9
DANN	Benign	0.66
PhyloP100		1.4
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: rs1125078; hg19: chr11-65809875; COSMIC: COSV61748585; COSMIC: COSV61748585;