rs372301143

Variant names:

• chr11-57415043-C-A
• rs372301143
• NM_199329.3:c.833G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-57415043-C-A
• chr11-57415043-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_199329.3(SLC43A3):​c.833G>T​(p.Arg278Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R278C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC43A3 NM_199329.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.57
• Publications: 0 publications found

Genes affected

SLC43A3 (HGNC:17466): (solute carrier family 43 member 3) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000254979 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.27357903).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_199329.3. 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
	SLC43A3	NM_199329.3	MANE Select	c.833G>T	p.Arg278Leu	missense	Exon 10 of 14	NP_955361.1	Q8NBI5-1
	SLC43A3	NM_001278206.2		c.872G>T	p.Arg291Leu	missense	Exon 10 of 14	NP_001265135.1	Q8NBI5-2
	SLC43A3	NM_001278201.2		c.833G>T	p.Arg278Leu	missense	Exon 10 of 14	NP_001265130.1	Q8NBI5-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC43A3	ENST00000395124.6	TSL:1 MANE Select	c.833G>T	p.Arg278Leu	missense	Exon 10 of 14	ENSP00000378556.1	Q8NBI5-1
	SLC43A3	ENST00000352187.5	TSL:1	c.833G>T	p.Arg278Leu	missense	Exon 10 of 14	ENSP00000337561.1	Q8NBI5-1
	SLC43A3	ENST00000395123.6	TSL:1	c.833G>T	p.Arg278Leu	missense	Exon 10 of 14	ENSP00000378555.2	Q8NBI5-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

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	0.15
BayesDel_addAF	Benign	-0.053	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	19
DANN	Benign	0.83
DEOGEN2	Benign	0.094	T
Eigen	Benign	-0.41
Eigen_PC	Benign	-0.26
FATHMM_MKL	Benign	0.71	D
LIST_S2	Benign	0.83	T
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.27	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	1.5	L
PhyloP100		4.6
PrimateAI	Benign	0.39	T
PROVEAN	Benign	0.67	N
REVEL	Benign	0.15
Sift	Benign	1.0	T
Sift4G	Benign	1.0	T
Polyphen		0.0010	B
Vest4		0.14
MutPred		0.62		Loss of methylation at R278 (P = 0.0165)
MVP		0.62
MPC		0.14
ClinPred		0.64	D
GERP RS		3.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.17
gMVP		0.50
Mutation Taster		=53/47	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs372301143; hg19: chr11-57182516;