dbSNP rs1059491: SULT1A2:p.Asn235Thr (chr16-28592334-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001054.4(SULT1A2):c.704A>C(p.Asn235Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.343 in 1,613,462 control chromosomes in the GnomAD database, including 99,598 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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.31 ( 8213 hom., cov: 32)

Exomes 𝑓: 0.35 ( 91385 hom. )

Consequence

SULT1A2
NM_001054.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.93

Variant links:

Genes affected

SULT1A2 (HGNC:11454): (sulfotransferase family 1A member 2) 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. Two alternatively spliced variants that encode the same protein have been described. [provided by RefSeq, Jul 2008]

SULT1A2 links:

ENSG00000288656 (HGNC:):

ENSG00000288656 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0042153).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT1A2	NM_001054.4 link	c.704A>C	p.Asn235Thr	missense_variant	Exon 7 of 8	ENST00000335715.9	NP_001045.2	P50226

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT1A2	ENST00000335715.9 link	c.704A>C	p.Asn235Thr	missense_variant	Exon 7 of 8	1	NM_001054.4	ENSP00000338742.4		P50226

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47408

AN:

151732

Hom.:

8202

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.169

Gnomad AMR

AF:

0.334

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.0694

Gnomad SAS

AF:

0.186

Gnomad FIN

AF:

0.451

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.368

Gnomad OTH

AF:

0.286

GnomAD3 exomes

AF:

0.317

AC:

79581

AN:

251216

Hom.:

14117

AF XY:

0.311

AC XY:

42227

AN XY:

135768

show subpopulations

Gnomad AFR exome

AF:

0.236

Gnomad AMR exome

AF:

0.384

Gnomad ASJ exome

AF:

0.278

Gnomad EAS exome

AF:

0.0623

Gnomad SAS exome

AF:

0.193

Gnomad FIN exome

AF:

0.445

Gnomad NFE exome

AF:

0.361

Gnomad OTH exome

AF:

0.325

GnomAD4 exome

AF:

0.346

AC:

506055

AN:

1461612

Hom.:

91385

Cov.:

105

AF XY:

0.342

AC XY:

248904

AN XY:

727120

show subpopulations

Gnomad4 AFR exome

AF:

0.227

Gnomad4 AMR exome

AF:

0.389

Gnomad4 ASJ exome

AF:

0.273

Gnomad4 EAS exome

AF:

0.0993

Gnomad4 SAS exome

AF:

0.196

Gnomad4 FIN exome

AF:

0.442

Gnomad4 NFE exome

AF:

0.368

Gnomad4 OTH exome

AF:

0.316

GnomAD4 genome

AF:

0.313

AC:

47454

AN:

151850

Hom.:

8213

Cov.:

AF XY:

0.312

AC XY:

23129

AN XY:

74202

show subpopulations

Gnomad4 AFR

AF:

0.232

Gnomad4 AMR

AF:

0.336

Gnomad4 ASJ

AF:

0.276

Gnomad4 EAS

AF:

0.0696

Gnomad4 SAS

AF:

0.185

Gnomad4 FIN

AF:

0.451

Gnomad4 NFE

AF:

0.368

Gnomad4 OTH

AF:

0.283

Alfa

AF:

0.342

Hom.:

4010

Bravo

AF:

0.303

TwinsUK

AF:

0.374

AC:

1386

ALSPAC

AF:

0.368

AC:

1417

ESP6500AA

AF:

0.246

AC:

1083

ESP6500EA

AF:

0.361

AC:

3103

ExAC

AF:

0.313

AC:

37956

Asia WGS

AF:

0.175

AC:

606

AN:

3478

EpiCase

AF:

0.330

EpiControl

AF:

0.325

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.62

BayesDel_addAF

Benign

-0.54

BayesDel_noAF

Benign

-0.40

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.61

D;T;T

Eigen

Pathogenic

0.74

Eigen_PC

Uncertain

0.66

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Pathogenic

0.98

D;.;D

MetaRNN

Benign

0.0042

T;T;T

MetaSVM

Benign

-0.94

MutationAssessor

Pathogenic

3.5

.;M;M

PrimateAI

Uncertain

0.53

PROVEAN

Pathogenic

-5.6

D;D;D

REVEL

Uncertain

0.34

Sift

Uncertain

0.012

D;D;D

Sift4G

Uncertain

0.0020

D;D;D

Polyphen

1.0

.;D;D

Vest4

0.17

MPC

0.43

ClinPred

0.027

GERP RS

5.0

Varity_R

0.85

gMVP

0.37

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over