Variant 16-28606193-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001055.4(SULT1A1):c.638G>A(p.Arg213His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 1,484,706 control chromosomes in the GnomAD database, including 93,546 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict 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 same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.30 ( 7555 hom., cov: 34)

Exomes 𝑓: 0.31 ( 85991 hom. )

Consequence

SULT1A1
NM_001055.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.02

Variant links:

Genes affected

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:

ENSG00000289755 (HGNC:):

ENSG00000289755 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=0.0036977232).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SULT1A1	NM_001055.4 linkuse as main transcript	c.638G>A	p.Arg213His	missense_variant	7/8	ENST00000314752.12	NP_001046.2	P50225-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SULT1A1	ENST00000314752.12 linkuse as main transcript	c.638G>A	p.Arg213His	missense_variant	7/8	1	NM_001055.4	ENSP00000321988.7		P50225-1

Frequencies

GnomAD3 genomes

AF:

0.295

AC:

43869

AN:

148526

Hom.:

7546

Cov.:

show subpopulations

Gnomad AFR

AF:

0.236

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.317

Gnomad ASJ

AF:

0.241

Gnomad EAS

AF:

0.0676

Gnomad SAS

AF:

0.191

Gnomad FIN

AF:

0.434

Gnomad MID

AF:

0.159

Gnomad NFE

AF:

0.337

Gnomad OTH

AF:

0.259

GnomAD3 exomes

AF:

0.224

AC:

46101

AN:

206082

Hom.:

10788

AF XY:

0.214

AC XY:

23666

AN XY:

110836

show subpopulations

Gnomad AFR exome

AF:

0.170

Gnomad AMR exome

AF:

0.318

Gnomad ASJ exome

AF:

0.167

Gnomad EAS exome

AF:

0.0389

Gnomad SAS exome

AF:

0.129

Gnomad FIN exome

AF:

0.379

Gnomad NFE exome

AF:

0.242

Gnomad OTH exome

AF:

0.231

GnomAD4 exome

AF:

0.307

AC:

410105

AN:

1336078

Hom.:

85991

Cov.:

AF XY:

0.303

AC XY:

201581

AN XY:

665188

show subpopulations

Gnomad4 AFR exome

AF:

0.209

Gnomad4 AMR exome

AF:

0.372

Gnomad4 ASJ exome

AF:

0.226

Gnomad4 EAS exome

AF:

0.0918

Gnomad4 SAS exome

AF:

0.185

Gnomad4 FIN exome

AF:

0.428

Gnomad4 NFE exome

AF:

0.324

Gnomad4 OTH exome

AF:

0.280

GnomAD4 genome

AF:

0.295

AC:

43911

AN:

148628

Hom.:

7555

Cov.:

AF XY:

0.295

AC XY:

21414

AN XY:

72468

show subpopulations

Gnomad4 AFR

AF:

0.236

Gnomad4 AMR

AF:

0.318

Gnomad4 ASJ

AF:

0.241

Gnomad4 EAS

AF:

0.0678

Gnomad4 SAS

AF:

0.191

Gnomad4 FIN

AF:

0.434

Gnomad4 NFE

AF:

0.337

Gnomad4 OTH

AF:

0.256

Alfa

AF:

0.317

Hom.:

1515

ESP6500AA

AF:

0.182

AC:

798

ESP6500EA

AF:

0.270

AC:

2322

ExAC

AF:

0.241

AC:

29256

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.091

BayesDel_addAF

Benign

-0.41

BayesDel_noAF

Benign

-0.22

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.65

D;.;D;D;D;.

Eigen

Benign

-0.45

Eigen_PC

Benign

-0.49

FATHMM_MKL

Benign

0.031

LIST_S2

Benign

0.12

.;T;T;.;.;T

MetaRNN

Benign

0.0037

T;T;T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.9

L;.;L;L;L;.

PrimateAI

Benign

0.30

PROVEAN

Uncertain

-2.9

D;D;D;D;D;D

REVEL

Uncertain

0.34

Sift

Benign

0.052

T;T;T;T;T;T

Sift4G

Benign

0.072

T;T;T;T;T;.

Polyphen

0.030

B;B;B;B;B;.

Vest4

0.050

MPC

1.8

ClinPred

0.011

GERP RS

2.2

Varity_R

0.31

gMVP

0.41

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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