dbSNP rs6839: ENSG00000289755:n.1661A>G (chr16-28605807-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000562058.5(ENSG00000289755):n.1661A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 1,596,498 control chromosomes in the GnomAD database, including 99,636 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.30 ( 7958 hom., cov: 35)

Exomes 𝑓: 0.34 ( 91678 hom. )

Consequence

ENSG00000289755
ENST00000562058.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.364

Publications

40 publications found

Variant links:

Genes affected

ENSG00000289755 (HGNC:):

ENSG00000289755 links:

SULT1A1 (HGNC:11453): (sulfotransferase family 1A 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 one of two phenol sulfotransferases with thermostable enzyme activity. Multiple alternatively spliced variants that encode two isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

SULT1A1 links:

Genome browser will be placed here

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=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT1A1	NM_001055.4 link	c.*14A>G		3_prime_UTR_variant	Exon 8 of 8	ENST00000314752.12	NP_001046.2	P50225-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT1A1	ENST00000314752.12 link	c.*14A>G		3_prime_UTR_variant	Exon 8 of 8	1	NM_001055.4	ENSP00000321988.7		P50225-1

Frequencies

GnomAD3 genomes

AF:

0.302

AC:

45359

AN:

150230

Hom.:

7950

Cov.:

show subpopulations

Gnomad AFR

AF:

0.224

Gnomad AMI

AF:

0.135

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.248

Gnomad EAS

AF:

0.0745

Gnomad SAS

AF:

0.204

Gnomad FIN

AF:

0.456

Gnomad MID

AF:

0.170

Gnomad NFE

AF:

0.352

Gnomad OTH

AF:

0.266

GnomAD2 exomes

AF:

0.311

AC:

77013

AN:

247864

AF XY:

0.305

show subpopulations

Gnomad AFR exome

AF:

0.229

Gnomad AMR exome

AF:

0.381

Gnomad ASJ exome

AF:

0.253

Gnomad EAS exome

AF:

0.0684

Gnomad FIN exome

AF:

0.451

Gnomad NFE exome

AF:

0.347

Gnomad OTH exome

AF:

0.313

GnomAD4 exome

AF:

0.337

AC:

487685

AN:

1446160

Hom.:

91678

Cov.:

AF XY:

0.334

AC XY:

240152

AN XY:

719516

show subpopulations

African (AFR)

AF:

0.221

AC:

7303

AN:

33088

American (AMR)

AF:

0.385

AC:

17069

AN:

44284

Ashkenazi Jewish (ASJ)

AF:

0.248

AC:

6432

AN:

25952

East Asian (EAS)

AF:

0.101

AC:

3986

AN:

39444

South Asian (SAS)

AF:

0.206

AC:

17575

AN:

85370

European-Finnish (FIN)

AF:

0.450

AC:

23939

AN:

53182

Middle Eastern (MID)

AF:

0.185

AC:

761

AN:

4106

European-Non Finnish (NFE)

AF:

0.356

AC:

392287

AN:

1101032

Other (OTH)

AF:

0.307

AC:

18333

AN:

59702

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.457

Heterozygous variant carriers

12718

25435

38153

50870

63588

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11992

23984

35976

47968

59960

<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:

0.302

AC:

45409

AN:

150338

Hom.:

7958

Cov.:

AF XY:

0.303

AC XY:

22231

AN XY:

73448

show subpopulations

African (AFR)

AF:

0.224

AC:

9167

AN:

40982

American (AMR)

AF:

0.323

AC:

4880

AN:

15116

Ashkenazi Jewish (ASJ)

AF:

0.248

AC:

851

AN:

3432

East Asian (EAS)

AF:

0.0747

AC:

383

AN:

5126

South Asian (SAS)

AF:

0.203

AC:

966

AN:

4756

European-Finnish (FIN)

AF:

0.456

AC:

4753

AN:

10428

Middle Eastern (MID)

AF:

0.175

AC:

AN:

286

European-Non Finnish (NFE)

AF:

0.352

AC:

23689

AN:

67236

Other (OTH)

AF:

0.265

AC:

547

AN:

2068

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

1055

2111

3166

4222

5277

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

462

924

1386

1848

2310

<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:

0.336

Hom.:

1990

Bravo

AF:

0.292

Asia WGS

AF:

0.194

AC:

673

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

5.1

(source)

DANN

Benign

0.64

PhyloP100

-0.36

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over