rs768133739

Variant names:

• chr11-62856322-A-C
• rs768133739
• ENST00000377890.6:c.53A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-62856322-A-C
• chr11-62856322-A-G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001012662.3(SLC3A2):​c.53A>C​(p.Gln18Pro) 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. 16/22 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. Q18R) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SLC3A2 NM_001012662.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• Publications: 0 publications found

Genes affected

SLC3A2 (HGNC:11026): (solute carrier family 3 member 2) This gene is a member of the solute carrier family and encodes a cell surface, transmembrane protein. The protein exists as the heavy chain of a heterodimer, covalently bound through di-sulfide bonds to one of several possible light chains. The encoded transporter plays a role in regulation of intracellular calcium levels and transports L-type amino acids. Alternatively spliced transcript variants, encoding different isoforms, have been characterized. [provided by RefSeq, Nov 2010]

SNHG1 (HGNC:32688): (small nucleolar RNA host gene 1) This locus represents a small nucleolar RNA host gene that produces multiple alternatively spliced long non-coding RNAs. This gene is upregulated in cancers and is thought to act as promoter of cell proliferation. This transcript negatively regulates tumor suppressor genes such as tumor protein p53. Expression of this locus may be a marker of tumor progression. [provided by RefSeq, Dec 2017]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.07194412).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001012662.3. 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
	SLC3A2	NM_001012662.3		c.53A>C	p.Gln18Pro	missense	Exon 1 of 12	NP_001012680.1	P08195-5
	SLC3A2	NM_002394.6		c.53A>C	p.Gln18Pro	missense	Exon 1 of 12	NP_002385.3
	SLC3A2	NM_001012664.3		c.53A>C	p.Gln18Pro	missense	Exon 1 of 10	NP_001012682.1	P08195-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC3A2	ENST00000377890.6	TSL:1	c.53A>C	p.Gln18Pro	missense	Exon 1 of 12	ENSP00000367122.2	P08195-1
	SLC3A2	ENST00000377889.6	TSL:1	c.53A>C	p.Gln18Pro	missense	Exon 1 of 10	ENSP00000367121.2	P08195-3
	SLC3A2	ENST00000538084.2	TSL:3	c.53A>C	p.Gln18Pro	missense	Exon 1 of 13	ENSP00000440001.2	P08195-4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.057
BayesDel_addAF	Benign	0.010	T
BayesDel_noAF	Benign	-0.22
CADD	Benign	14
DANN	Benign	0.91
DEOGEN2	Benign	0.24	T
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.018	N
LIST_S2	Benign	0.55	T
M_CAP	Benign	0.049	D
MetaRNN	Benign	0.072	T
MetaSVM	Uncertain	0.39	D
MutationAssessor	Benign	0.0	N
PhyloP100		0.34
PrimateAI	Benign	0.40	T
PROVEAN	Benign	0.31	N
REVEL	Benign	0.21
Sift	Benign	0.40	T
Sift4G	Uncertain	0.030	D
Polyphen		0.0	B
Vest4		0.21
MutPred		0.13		Gain of glycosylation at Q18 (P = 0.1016)
MVP		0.50
MPC		1.5
ClinPred		0.096	T
GERP RS		-3.8
PromoterAI		0.013	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.8
Varity_R		0.063
gMVP		0.18
Mutation Taster		=97/3	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: rs768133739; hg19: chr11-62623794;