chr11-66042292-C-T

Variant names:

• chr11-66042292-C-T
• rs3814744
• NM_033036.3:c.*215G>A

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.*215G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 512,140 control chromosomes in the GnomAD database, including 6,819 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.17 (2331 hom., cov: 33)
  • Exomes 𝑓: 0.15 (4488 hom.)
• Consequence: GAL3ST3 NM_033036.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.108
• Publications: 7 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=-0.86).
• BP6: Variant 11-66042292-C-T is Benign according to our data. Variant chr11-66042292-C-T is described in ClinVar as Benign. ClinVar VariationId is 1269158.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 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.*215G>A		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.*215G>A		3_prime_UTR	Exon 3 of 3	ENSP00000308591.3	Q96A11
	GAL3ST3	ENST00000882250.1		c.*215G>A		3_prime_UTR	Exon 3 of 3	ENSP00000552309.1
	GAL3ST3	ENST00000882251.1		c.*215G>A		3_prime_UTR	Exon 4 of 4	ENSP00000552310.1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26127 AN: 152082 Hom.: 2330 Cov.: 33

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.188

GnomAD4 exome AF: 0.152 AC: 54643 AN: 359940 Hom.: 4488 Cov.: 3 AF XY: 0.153 AC XY: 28628 AN XY: 187088

African (AFR) AF: 0.210 AC: 1662 AN: 7912

American (AMR) AF: 0.116 AC: 1137 AN: 9790

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 1979 AN: 11688

East Asian (EAS) AF: 0.0946 AC: 2303 AN: 24352

South Asian (SAS) AF: 0.158 AC: 4369 AN: 27704

European-Finnish (FIN) AF: 0.150 AC: 4158 AN: 27748

Middle Eastern (MID) AF: 0.219 AC: 373 AN: 1706

European-Non Finnish (NFE) AF: 0.155 AC: 35218 AN: 227004

Other (OTH) AF: 0.156 AC: 3444 AN: 22036

GnomAD4 genome AF: 0.172 AC: 26139 AN: 152200 Hom.: 2331 Cov.: 33 AF XY: 0.172 AC XY: 12774 AN XY: 74412

African (AFR) AF: 0.212 AC: 8804 AN: 41532

American (AMR) AF: 0.149 AC: 2280 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 624 AN: 3470

East Asian (EAS) AF: 0.111 AC: 573 AN: 5168

South Asian (SAS) AF: 0.173 AC: 834 AN: 4822

European-Finnish (FIN) AF: 0.153 AC: 1623 AN: 10600

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.159 AC: 10832 AN: 67992

Other (OTH) AF: 0.192 AC: 405 AN: 2114

Alfa AF: 0.166 Hom.: 2143

Bravo AF: 0.171

Asia WGS AF: 0.174 AC: 607 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	-0.86
CADD	Benign	3.4
DANN	Benign	0.65
PhyloP100		0.11
Mutation Taster		=99/1	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: rs3814744; hg19: chr11-65809763; COSMIC: COSV61749929; COSMIC: COSV61749929;