Variant rs1402467 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_006588.4(SULT1C4):c.15C>G(p.Asp5Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 1,612,738 control chromosomes in the GnomAD database, including 75,108 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.39 ( 16119 hom., cov: 32)

Exomes 𝑓: 0.27 ( 58989 hom. )

Consequence

SULT1C4
NM_006588.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.874

Variant links:

Genes affected

SULT1C4 (HGNC:11457): (sulfotransferase family 1C member 4) 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 belongs to the SULT1 subfamily, responsible for transferring a sulfo moiety from PAPS to phenol-containing compounds. [provided by RefSeq, Jul 2008]

SULT1C4 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=9.924704E-7).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SULT1C4	NM_006588.4 link	c.15C>G	p.Asp5Glu	missense_variant	1/7	ENST00000272452.7	NP_006579.2	O75897-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SULT1C4	ENST00000272452.7 link	c.15C>G	p.Asp5Glu	missense_variant	1/7	1	NM_006588.4	ENSP00000272452.2	O75897-1
SULT1C4	ENST00000409309.3 link	c.15C>G	p.Asp5Glu	missense_variant	1/5	1		ENSP00000387225.3	O75897-2
SULT1C4	ENST00000494122.1 link	n.442C>G		non_coding_transcript_exon_variant	1/2	1

Frequencies

GnomAD3 genomes

AF:

0.392

AC:

59613

AN:

151918

Hom.:

16061

Cov.:

show subpopulations

Gnomad AFR

AF:

0.766

Gnomad AMI

AF:

0.198

Gnomad AMR

AF:

0.228

Gnomad ASJ

AF:

0.248

Gnomad EAS

AF:

0.110

Gnomad SAS

AF:

0.425

Gnomad FIN

AF:

0.337

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.241

Gnomad OTH

AF:

0.348

GnomAD3 exomes

AF:

0.283

AC:

71070

AN:

251050

Hom.:

13431

AF XY:

0.287

AC XY:

38877

AN XY:

135694

show subpopulations

Gnomad AFR exome

AF:

0.782

Gnomad AMR exome

AF:

0.150

Gnomad ASJ exome

AF:

0.252

Gnomad EAS exome

AF:

0.0712

Gnomad SAS exome

AF:

0.415

Gnomad FIN exome

AF:

0.333

Gnomad NFE exome

AF:

0.245

Gnomad OTH exome

AF:

0.266

GnomAD4 exome

AF:

0.266

AC:

387856

AN:

1460702

Hom.:

58989

Cov.:

AF XY:

0.269

AC XY:

195320

AN XY:

726716

show subpopulations

Gnomad4 AFR exome

AF:

0.794

Gnomad4 AMR exome

AF:

0.163

Gnomad4 ASJ exome

AF:

0.245

Gnomad4 EAS exome

AF:

0.159

Gnomad4 SAS exome

AF:

0.411

Gnomad4 FIN exome

AF:

0.327

Gnomad4 NFE exome

AF:

0.242

Gnomad4 OTH exome

AF:

0.288

GnomAD4 genome

AF:

0.393

AC:

59728

AN:

152036

Hom.:

16119

Cov.:

AF XY:

0.394

AC XY:

29323

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.767

Gnomad4 AMR

AF:

0.228

Gnomad4 ASJ

AF:

0.248

Gnomad4 EAS

AF:

0.110

Gnomad4 SAS

AF:

0.424

Gnomad4 FIN

AF:

0.337

Gnomad4 NFE

AF:

0.241

Gnomad4 OTH

AF:

0.355

Alfa

AF:

0.261

Hom.:

4709

Bravo

AF:

0.393

TwinsUK

AF:

0.250

AC:

926

ALSPAC

AF:

0.237

AC:

912

ESP6500AA

AF:

0.767

AC:

3378

ESP6500EA

AF:

0.246

AC:

2118

ExAC

AF:

0.298

AC:

36195

Asia WGS

AF:

0.379

AC:

1319

AN:

3478

EpiCase

AF:

0.242

EpiControl

AF:

0.244

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.85

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.26

DANN

Benign

0.60

DEOGEN2

Benign

0.0039

T;.

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.0037

LIST_S2

Benign

0.14

T;T

MetaRNN

Benign

9.9e-7

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.55

N;N

PrimateAI

Benign

0.43

PROVEAN

Benign

0.71

N;N

REVEL

Benign

0.068

Sift

Benign

0.94

T;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0

B;.

Vest4

0.011

MutPred

0.062

Gain of helix (P = 0.0696);Gain of helix (P = 0.0696);

MPC

0.23

ClinPred

0.00089

GERP RS

-1.8

Varity_R

0.078

gMVP

0.65

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