Variant chr2-108247302-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001320878.2(SULT1C3):c.108G>A(p.Trp36*) variant causes a stop gained change. The variant allele was found at a frequency of 0.0187 in 1,598,718 control chromosomes in the GnomAD database, including 452 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.016 ( 22 hom., cov: 32)

Exomes 𝑓: 0.019 ( 430 hom. )

Consequence

SULT1C3
NM_001320878.2 stop_gained

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 4.18

Variant links:

Genes affected

SULT1C3 (HGNC:33543): (sulfotransferase family 1C member 3) Enables 3'-phosphoadenosine 5'-phosphosulfate binding activity and sulfotransferase activity. Involved in 3'-phosphoadenosine 5'-phosphosulfate metabolic process; cholesterol metabolic process; and xenobiotic metabolic process. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

SULT1C3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT1C3	NM_001320878.2 link	c.108G>A	p.Trp36*	stop_gained	Exon 2 of 8	ENST00000681802.2	NP_001307807.1	Q6IMI6-2
SULT1C3	NM_001008743.3 link	c.108G>A	p.Trp36*	stop_gained	Exon 2 of 8		NP_001008743.1	Q6IMI6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT1C3	ENST00000681802.2 link	c.108G>A	p.Trp36*	stop_gained	Exon 2 of 8		NM_001320878.2	ENSP00000505748.1		Q6IMI6-2
SULT1C3	ENST00000329106.3 link	c.108G>A	p.Trp36*	stop_gained	Exon 2 of 8	2		ENSP00000333310.2		Q6IMI6-1

Frequencies

GnomAD3 genomes

AF:

0.0159

AC:

2420

AN:

152108

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0103

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0119

Gnomad ASJ

AF:

0.0130

Gnomad EAS

AF:

0.00520

Gnomad SAS

AF:

0.0465

Gnomad FIN

AF:

0.0315

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0167

Gnomad OTH

AF:

0.0191

GnomAD3 exomes

AF:

0.0216

AC:

5278

AN:

244308

Hom.:

116

AF XY:

0.0237

AC XY:

3135

AN XY:

132108

show subpopulations

Gnomad AFR exome

AF:

0.0109

Gnomad AMR exome

AF:

0.00910

Gnomad ASJ exome

AF:

0.0113

Gnomad EAS exome

AF:

0.00429

Gnomad SAS exome

AF:

0.0586

Gnomad FIN exome

AF:

0.0346

Gnomad NFE exome

AF:

0.0185

Gnomad OTH exome

AF:

0.0179

GnomAD4 exome

AF:

0.0190

AC:

27510

AN:

1446492

Hom.:

430

Cov.:

AF XY:

0.0203

AC XY:

14569

AN XY:

718922

show subpopulations

Gnomad4 AFR exome

AF:

0.00934

Gnomad4 AMR exome

AF:

0.00995

Gnomad4 ASJ exome

AF:

0.00990

Gnomad4 EAS exome

AF:

0.00390

Gnomad4 SAS exome

AF:

0.0560

Gnomad4 FIN exome

AF:

0.0328

Gnomad4 NFE exome

AF:

0.0171

Gnomad4 OTH exome

AF:

0.0172

GnomAD4 genome

AF:

0.0159

AC:

2428

AN:

152226

Hom.:

Cov.:

AF XY:

0.0173

AC XY:

1288

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.0103

Gnomad4 AMR

AF:

0.0119

Gnomad4 ASJ

AF:

0.0130

Gnomad4 EAS

AF:

0.00540

Gnomad4 SAS

AF:

0.0469

Gnomad4 FIN

AF:

0.0315

Gnomad4 NFE

AF:

0.0167

Gnomad4 OTH

AF:

0.0194

Alfa

AF:

0.0161

Hom.:

Bravo

AF:

0.0138

TwinsUK

AF:

0.0175

AC:

ALSPAC

AF:

0.0179

AC:

ESP6500AA

AF:

0.0120

AC:

ESP6500EA

AF:

0.0171

AC:

147

ExAC

AF:

0.0241

AC:

2931

Asia WGS

AF:

0.0300

AC:

103

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: ExAC frequency -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.011

BayesDel_noAF

Pathogenic

0.25

CADD

Pathogenic

DANN

Uncertain

0.99

Eigen

Uncertain

0.45

Eigen_PC

Benign

0.19

FATHMM_MKL

Benign

0.60

Vest4

0.082

GERP RS

4.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.38

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.38

Position offset: -4

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over