Genetic Variant SULT1E1:c.497-10C>G (chr4-69847802-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005420.3(SULT1E1):c.497-10C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 1,583,348 control chromosomes in the GnomAD database, including 11,928 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.12 ( 1151 hom., cov: 32)

Exomes 𝑓: 0.12 ( 10777 hom. )

Consequence

SULT1E1
NM_005420.3 intron

Scores

Splicing: ADA: 0.006855

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.100

Publications

9 publications found

Variant links:

Genes affected

SULT1E1 (HGNC:11377): (sulfotransferase family 1E member 1) Sulfotransferase enzymes catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs, and xenobiotic compounds. These cytosolic enzymes are different in their tissue distributions and substrate specificities. The gene structure (number and length of exons) is similar among family members. This gene encodes a protein that transfers a sulfo moiety to and from estrone, which may control levels of estrogen receptors. [provided by RefSeq, Jul 2008]

SULT1E1 links:

ENSG00000284695 (HGNC:):

ENSG00000284695 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005420.3. 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
	SULT1E1	NM_005420.3	MANE Select	c.497-10C>G		intron	N/A	NP_005411.1	Q53X91

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SULT1E1	ENST00000226444.4	TSL:1 MANE Select	c.497-10C>G	intron	N/A	ENSP00000226444.3	P49888
SULT1E1	ENST00000904222.1		c.545-10C>G	intron	N/A	ENSP00000574281.1
SULT1E1	ENST00000904212.1		c.497-10C>G	intron	N/A	ENSP00000574271.1

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17518

AN:

151238

Hom.:

1149

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0954

Gnomad AMI

AF:

0.0945

Gnomad AMR

AF:

0.0891

Gnomad ASJ

AF:

0.161

Gnomad EAS

AF:

0.000773

Gnomad SAS

AF:

0.0467

Gnomad FIN

AF:

0.240

Gnomad MID

AF:

0.178

Gnomad NFE

AF:

0.126

Gnomad OTH

AF:

0.125

GnomAD2 exomes

AF:

0.108

AC:

26451

AN:

245216

AF XY:

0.108

show subpopulations

Gnomad AFR exome

AF:

0.0923

Gnomad AMR exome

AF:

0.0591

Gnomad ASJ exome

AF:

0.161

Gnomad EAS exome

AF:

0.000111

Gnomad FIN exome

AF:

0.227

Gnomad NFE exome

AF:

0.131

Gnomad OTH exome

AF:

0.121

GnomAD4 exome

AF:

0.116

AC:

166284

AN:

1431992

Hom.:

10777

Cov.:

AF XY:

0.115

AC XY:

82013

AN XY:

713576

show subpopulations

African (AFR)

AF:

0.0959

AC:

3121

AN:

32536

American (AMR)

AF:

0.0645

AC:

2828

AN:

43830

Ashkenazi Jewish (ASJ)

AF:

0.163

AC:

4170

AN:

25654

East Asian (EAS)

AF:

0.000307

AC:

AN:

39114

South Asian (SAS)

AF:

0.0469

AC:

3974

AN:

84688

European-Finnish (FIN)

AF:

0.224

AC:

11821

AN:

52832

Middle Eastern (MID)

AF:

0.185

AC:

1053

AN:

5694

European-Non Finnish (NFE)

AF:

0.122

AC:

132363

AN:

1088368

Other (OTH)

AF:

0.117

AC:

6942

AN:

59276

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

6727

13454

20181

26908

33635

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4554

9108

13662

18216

22770

<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:

0.116

AC:

17531

AN:

151356

Hom.:

1151

Cov.:

AF XY:

0.118

AC XY:

8752

AN XY:

73958

show subpopulations

African (AFR)

AF:

0.0955

AC:

3952

AN:

41392

American (AMR)

AF:

0.0891

AC:

1351

AN:

15164

Ashkenazi Jewish (ASJ)

AF:

0.161

AC:

556

AN:

3456

East Asian (EAS)

AF:

0.000775

AC:

AN:

5164

South Asian (SAS)

AF:

0.0463

AC:

222

AN:

4796

European-Finnish (FIN)

AF:

0.240

AC:

2527

AN:

10528

Middle Eastern (MID)

AF:

0.182

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.126

AC:

8520

AN:

67550

Other (OTH)

AF:

0.124

AC:

260

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

771

1542

2314

3085

3856

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

194

388

582

776

970

<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:

0.126

Hom.:

234

Bravo

AF:

0.106

Asia WGS

AF:

0.0310

AC:

107

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

9.3

(source)

DANN

Benign

0.70

PhyloP100

0.10

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0069

dbscSNV1_RF

Benign

0.14

SpliceAI score (max)

0.19

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

Computational scores

Splicing

Publications

Other links and lift over