chr22-30557308-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001318104.2(GAL3ST1):c.85G>A(p.Val29Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 1,613,592 control chromosomes in the GnomAD database, including 78,135 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 8059 hom., cov: 33)

Exomes 𝑓: 0.31 ( 70076 hom. )

Consequence

GAL3ST1
NM_001318104.2 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.52

Publications

39 publications found

Variant links:

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]

GAL3ST1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (MetaRNN=0.0048956573).

BP6

Variant 22-30557308-C-T is Benign according to our data. Variant chr22-30557308-C-T is described in ClinVar as Benign. ClinVar VariationId is 1230435.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318104.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
GAL3ST1	NM_001318104.2	MANE Select	c.85G>A	p.Val29Met	missense	Exon 3 of 4	NP_001305033.1
GAL3ST1	NM_001318107.2		c.85G>A	p.Val29Met	missense	Exon 3 of 4	NP_001305036.1
GAL3ST1	NM_001318114.2		c.85G>A	p.Val29Met	missense	Exon 2 of 3	NP_001305043.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
GAL3ST1	ENST00000406361.6	TSL:2 MANE Select	c.85G>A	p.Val29Met	missense	Exon 3 of 4	ENSP00000385207.1
GAL3ST1	ENST00000338911.6	TSL:1	c.85G>A	p.Val29Met	missense	Exon 1 of 2	ENSP00000343234.5
GAL3ST1	ENST00000401975.5	TSL:1	c.85G>A	p.Val29Met	missense	Exon 3 of 4	ENSP00000384388.1

Frequencies

GnomAD3 genomes

AF:

0.324

AC:

49307

AN:

152038

Hom.:

8062

Cov.:

show subpopulations

Gnomad AFR

AF:

0.362

Gnomad AMI

AF:

0.346

Gnomad AMR

AF:

0.286

Gnomad ASJ

AF:

0.382

Gnomad EAS

AF:

0.335

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.323

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.313

Gnomad OTH

AF:

0.336

GnomAD2 exomes

AF:

0.303

AC:

76041

AN:

251104

AF XY:

0.300

show subpopulations

Gnomad AFR exome

AF:

0.368

Gnomad AMR exome

AF:

0.228

Gnomad ASJ exome

AF:

0.379

Gnomad EAS exome

AF:

0.325

Gnomad FIN exome

AF:

0.338

Gnomad NFE exome

AF:

0.323

Gnomad OTH exome

AF:

0.309

GnomAD4 exome

AF:

0.307

AC:

448410

AN:

1461436

Hom.:

70076

Cov.:

AF XY:

0.304

AC XY:

221290

AN XY:

727014

show subpopulations

African (AFR)

AF:

0.371

AC:

12417

AN:

33460

American (AMR)

AF:

0.230

AC:

10282

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.383

AC:

10000

AN:

26130

East Asian (EAS)

AF:

0.333

AC:

13236

AN:

39696

South Asian (SAS)

AF:

0.215

AC:

18543

AN:

86246

European-Finnish (FIN)

AF:

0.329

AC:

17572

AN:

53406

Middle Eastern (MID)

AF:

0.267

AC:

1536

AN:

5762

European-Non Finnish (NFE)

AF:

0.311

AC:

346036

AN:

1111644

Other (OTH)

AF:

0.311

AC:

18788

AN:

60376

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

16198

32396

48594

64792

80990

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11228

22456

33684

44912

56140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.324

AC:

49314

AN:

152156

Hom.:

8059

Cov.:

AF XY:

0.322

AC XY:

23951

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.362

AC:

15029

AN:

41522

American (AMR)

AF:

0.286

AC:

4372

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.382

AC:

1327

AN:

3472

East Asian (EAS)

AF:

0.335

AC:

1738

AN:

5182

South Asian (SAS)

AF:

0.210

AC:

1015

AN:

4830

European-Finnish (FIN)

AF:

0.323

AC:

3419

AN:

10590

Middle Eastern (MID)

AF:

0.337

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.313

AC:

21301

AN:

67958

Other (OTH)

AF:

0.331

AC:

699

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1731

3461

5192

6922

8653

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

484

968

1452

1936

2420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.320

Hom.:

37711

Bravo

AF:

0.330

TwinsUK

AF:

0.311

AC:

1155

ALSPAC

AF:

0.313

AC:

1205

ESP6500AA

AF:

0.374

AC:

1647

ESP6500EA

AF:

0.318

AC:

2732

ExAC

AF:

0.306

AC:

37191

Asia WGS

AF:

0.271

AC:

947

AN:

3478

EpiCase

AF:

0.321

EpiControl

AF:

0.327

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.47

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.063

Eigen

Benign

-0.58

Eigen_PC

Benign

-0.44

FATHMM_MKL

Benign

0.60

LIST_S2

Uncertain

0.91

MetaRNN

Benign

0.0049

MetaSVM

Benign

-0.89

MutationAssessor

Benign

0.55

PhyloP100

1.5

PrimateAI

Benign

0.41

PROVEAN

Benign

0.16

REVEL

Benign

0.034

Sift

Benign

0.051

Sift4G

Uncertain

0.052

Polyphen

0.14

Vest4

0.098

MPC

0.92

ClinPred

0.020

GERP RS

1.1

PromoterAI

0.043

Neutral

(source)

Varity_R

0.030

gMVP

0.48

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

ClinVar submissions as Germline

Computational scores

Splicing

Publications

Other links and lift over