dbSNP rs138060: SULT4A1:c.743-814T>G (chr22-43826927-A-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_014351.4(SULT4A1):c.743-814T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 985,146 control chromosomes in the GnomAD database, including 116,955 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 0.49 ( 18785 hom., cov: 33)

Exomes 𝑓: 0.48 ( 98170 hom. )

Consequence

SULT4A1
NM_014351.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.409

Publications

11 publications found

Variant links:

Genes affected

SULT4A1 (HGNC:14903): (sulfotransferase family 4A member 1) This gene encodes a member of the sulfotransferase family. The encoded protein is a brain-specific sulfotransferase believed to be involved in the metabolism of neurotransmitters. Polymorphisms in this gene may be associated with susceptibility to schizophrenia. [provided by RefSeq, Jul 2008]

SULT4A1 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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT4A1	NM_014351.4 link	c.743-814T>G		intron_variant	Intron 6 of 6	ENST00000330884.9	NP_055166.1
SULT4A1	XM_011530121.2 link	c.404-814T>G		intron_variant	Intron 3 of 3		XP_011528423.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
SULT4A1	ENST00000330884.9 link	c.743-814T>G	intron_variant	Intron 6 of 6	1	NM_014351.4	ENSP00000332565.4
SULT4A1	ENST00000422525.1 link	n.*86+587T>G	intron_variant	Intron 7 of 7	1		ENSP00000388285.1
SULT4A1	ENST00000432404.5 link	n.*384-814T>G	intron_variant	Intron 5 of 5	5		ENSP00000414220.1

Frequencies

GnomAD3 genomes

AF:

0.494

AC:

75003

AN:

151952

Hom.:

18759

Cov.:

show subpopulations

Gnomad AFR

AF:

0.495

Gnomad AMI

AF:

0.590

Gnomad AMR

AF:

0.433

Gnomad ASJ

AF:

0.497

Gnomad EAS

AF:

0.489

Gnomad SAS

AF:

0.649

Gnomad FIN

AF:

0.492

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.494

Gnomad OTH

AF:

0.491

GnomAD4 exome

AF:

0.485

AC:

403884

AN:

833076

Hom.:

98170

Cov.:

AF XY:

0.485

AC XY:

186419

AN XY:

384696

show subpopulations

African (AFR)

AF:

0.510

AC:

8054

AN:

15784

American (AMR)

AF:

0.391

AC:

385

AN:

984

Ashkenazi Jewish (ASJ)

AF:

0.520

AC:

2678

AN:

5152

East Asian (EAS)

AF:

0.477

AC:

1731

AN:

3630

South Asian (SAS)

AF:

0.648

AC:

10666

AN:

16460

European-Finnish (FIN)

AF:

0.536

AC:

148

AN:

276

Middle Eastern (MID)

AF:

0.533

AC:

863

AN:

1620

European-Non Finnish (NFE)

AF:

0.480

AC:

365642

AN:

761872

Other (OTH)

AF:

0.502

AC:

13717

AN:

27298

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

12314

24628

36941

49255

61569

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14890

29780

44670

59560

74450

<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:

0.494

AC:

75076

AN:

152070

Hom.:

18785

Cov.:

AF XY:

0.495

AC XY:

36794

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.496

AC:

20575

AN:

41506

American (AMR)

AF:

0.433

AC:

6610

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.497

AC:

1725

AN:

3472

East Asian (EAS)

AF:

0.489

AC:

2532

AN:

5176

South Asian (SAS)

AF:

0.648

AC:

3120

AN:

4816

European-Finnish (FIN)

AF:

0.492

AC:

5196

AN:

10558

Middle Eastern (MID)

AF:

0.537

AC:

158

AN:

294

European-Non Finnish (NFE)

AF:

0.494

AC:

33579

AN:

67960

Other (OTH)

AF:

0.494

AC:

1045

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1988

3977

5965

7954

9942

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

680

1360

2040

2720

3400

<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:

0.490

Hom.:

55616

Bravo

AF:

0.481

Asia WGS

AF:

0.559

AC:

1943

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.5

(source)

DANN

Benign

0.33

PhyloP100

-0.41

Mutation Taster

=99/1

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