rs756386313

Variant names:

• chr2-108255690-C-A
• rs756386313
• NM_001320878.2:c.518C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-108255690-C-A
• chr2-108255690-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001320878.2(SULT1C3):​c.518C>A​(p.Ser173Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. S173C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SULT1C3 NM_001320878.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.35959715).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT1C3	NM_001320878.2	c.518C>A	p.Ser173Tyr	missense_variant	Exon 5 of 8	ENST00000681802.2	NP_001307807.1
SULT1C3	NM_001008743.3	c.518C>A	p.Ser173Tyr	missense_variant	Exon 5 of 8		NP_001008743.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT1C3	ENST00000681802.2	c.518C>A	p.Ser173Tyr	missense_variant	Exon 5 of 8		NM_001320878.2	ENSP00000505748.1
SULT1C3	ENST00000329106.3	c.518C>A	p.Ser173Tyr	missense_variant	Exon 5 of 8	2		ENSP00000333310.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.18
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.59
CADD	Benign	15
DANN	Uncertain	0.98
DEOGEN2	Benign	0.22	T
Eigen	Benign	-0.65
Eigen_PC	Benign	-0.86
FATHMM_MKL	Benign	0.032	N
LIST_S2	Uncertain	0.87	D
M_CAP	Benign	0.0039	T
MetaRNN	Benign	0.36	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Pathogenic	3.0	M
PrimateAI	Benign	0.30	T
PROVEAN	Uncertain	-3.1	D
REVEL	Benign	0.071
Sift	Uncertain	0.016	D
Sift4G	Uncertain	0.027	D
Polyphen		0.59	P
Vest4		0.20
MutPred		0.45		Gain of solvent accessibility (P = 0.0739);
MVP		0.31
MPC		0.27
ClinPred		0.60	D
GERP RS		1.5
Varity_R		0.20
gMVP		0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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

Other links and lift over

dbSNP: rs756386313; hg19: chr2-108872146;