Genetic Variant GAL3ST3:c.*103G>T (chr11-66042404-C-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.36

Variant links:

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]

GAL3ST3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAL3ST3	NM_033036.3 link	c.*103G>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000312006.5	NP_149025.1	Q96A11
GAL3ST3	XM_017018519.2 link	c.*103G>T		3_prime_UTR_variant	Exon 2 of 2		XP_016874008.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAL3ST3	ENST00000312006 link	c.*103G>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_033036.3	ENSP00000308591.3		Q96A11
GAL3ST3	ENST00000527878 link	c.*103G>T		3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000434829.1		Q96A11

Frequencies

GnomAD3 genomes

AF:

0.759

AC:

115409

AN:

151964

Hom.:

45000

Cov.:

show subpopulations

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.:

AF XY:

0.840

AC XY:

313155

AN XY:

372650

show subpopulations

Gnomad4 AFR exome

AF:

0.563

Gnomad4 AMR exome

AF:

0.856

Gnomad4 ASJ exome

AF:

0.833

Gnomad4 EAS exome

AF:

0.809

Gnomad4 SAS exome

AF:

0.831

Gnomad4 FIN exome

AF:

0.846

Gnomad4 NFE exome

AF:

0.851

Gnomad4 OTH exome

AF:

0.822

GnomAD4 genome

AF:

0.759

AC:

115487

AN:

152082

Hom.:

45031

Cov.:

AF XY:

0.762

AC XY:

56675

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.569

Gnomad4 AMR

AF:

0.812

Gnomad4 ASJ

AF:

0.820

Gnomad4 EAS

AF:

0.777

Gnomad4 SAS

AF:

0.820

Gnomad4 FIN

AF:

0.847

Gnomad4 NFE

AF:

0.839

Gnomad4 OTH

AF:

0.753

Alfa

AF:

0.790

Hom.:

7426

Bravo

AF:

0.749

Asia WGS

AF:

0.770

AC:

2676

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 11, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.9

DANN

Benign

0.66

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over