NM_001320878.2:c.11T>C

Variant names:

• chr2-108247205-T-C
• rs145344319
• NM_001320878.2:c.11T>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001320878.2(SULT1C3):​c.11T>C​(p.Ile4Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00171 in 1,522,032 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0012 (1 hom., cov: 32)
  • Exomes 𝑓: 0.0018 (3 hom.)
• Consequence: SULT1C3 NM_001320878.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.421
• Publications: 6 publications found

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]

ENSG00000294676 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0070406795).
• BS2: High Homozygotes in GnomAdExome4 at 3 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001320878.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT1C3	NM_001320878.2	MANE Select	c.11T>C	p.Ile4Thr	missense	Exon 2 of 8	NP_001307807.1	Q6IMI6-2
	SULT1C3	NM_001008743.3		c.11T>C	p.Ile4Thr	missense	Exon 2 of 8	NP_001008743.1	Q6IMI6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT1C3	ENST00000681802.2	MANE Select	c.11T>C	p.Ile4Thr	missense	Exon 2 of 8	ENSP00000505748.1	Q6IMI6-2
	SULT1C3	ENST00000329106.3	TSL:2	c.11T>C	p.Ile4Thr	missense	Exon 2 of 8	ENSP00000333310.2	Q6IMI6-1
	SULT1C3	ENST00000899643.1		c.11T>C	p.Ile4Thr	missense	Exon 2 of 9	ENSP00000569702.1

Frequencies

GnomAD3 genomes AF: 0.00122 AC: 185 AN: 152080 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.000507

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000787

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00190

Gnomad OTH AF: 0.00239

GnomAD2 exomes AF: 0.00132 AC: 278 AN: 210834 AF XY: 0.00145

Gnomad AFR exome AF: 0.0000690

Gnomad AMR exome AF: 0.000900

Gnomad ASJ exome AF: 0.00413

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00170

Gnomad OTH exome AF: 0.00123

GnomAD4 exome AF: 0.00176 AC: 2416 AN: 1369834 Hom.: 3 Cov.: 32 AF XY: 0.00182 AC XY: 1229 AN XY: 675140

African (AFR) AF: 0.000333 AC: 10 AN: 30034

American (AMR) AF: 0.00139 AC: 46 AN: 33192

Ashkenazi Jewish (ASJ) AF: 0.00225 AC: 52 AN: 23120

East Asian (EAS) AF: 0.0000533 AC: 2 AN: 37528

South Asian (SAS) AF: 0.00205 AC: 143 AN: 69720

European-Finnish (FIN) AF: 0.0000786 AC: 4 AN: 50894

Middle Eastern (MID) AF: 0.00406 AC: 22 AN: 5418

European-Non Finnish (NFE) AF: 0.00188 AC: 1999 AN: 1063876

Other (OTH) AF: 0.00246 AC: 138 AN: 56052

GnomAD4 genome AF: 0.00122 AC: 185 AN: 152198 Hom.: 1 Cov.: 32 AF XY: 0.00124 AC XY: 92 AN XY: 74412

African (AFR) AF: 0.000506 AC: 21 AN: 41532

American (AMR) AF: 0.000786 AC: 12 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.000865 AC: 3 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00291 AC: 14 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10608

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00190 AC: 129 AN: 68010

Other (OTH) AF: 0.00236 AC: 5 AN: 2116

Alfa AF: 0.00195 Hom.: 3

Bravo AF: 0.00125

TwinsUK AF: 0.00189 AC: 7

ALSPAC AF: 0.00259 AC: 10

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.00291 AC: 25

ExAC AF: 0.00137 AC: 166

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.061
BayesDel_addAF	Benign	-0.69	T
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.037
DANN	Benign	0.50
DEOGEN2	Benign	0.0015	T
Eigen	Benign	-2.0
Eigen_PC	Benign	-2.1
FATHMM_MKL	Benign	0.0073	N
LIST_S2	Benign	0.33	T
M_CAP	Benign	0.0015	T
MetaRNN	Benign	0.0070	T
MetaSVM	Benign	-0.92	T
MutationAssessor	Benign	0.0	N
PhyloP100		-0.42
PrimateAI	Benign	0.46	T
PROVEAN	Benign	-0.40	N
REVEL	Benign	0.023
Sift	Benign	0.25	T
Sift4G	Benign	0.34	T
Polyphen		0.0	B
Vest4		0.037
MVP		0.15
MPC		0.071
ClinPred		0.0040	T
GERP RS		-5.4
Varity_R		0.031
gMVP		0.30
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs145344319; hg19: chr2-108863661;