ENST00000377890.6:c.299-4182A>G

Variant names:

• chr11-62876837-A-G
• rs1461175319
• ENST00000377890.6:c.299-4182A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000377890.6(SLC3A2):​c.299-4182A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000817 in 856,940 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.000026 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000043 (0 hom.)
• Consequence: SLC3A2 ENST00000377890.6 intron
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.0380
• 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]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.039947778).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000377890.6. 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.259A>G	p.Ile87Val	missense	Exon 3 of 12	NP_001012680.1	P08195-5
	SLC3A2	NM_002394.6		c.299-4182A>G		intron	N/A	NP_002385.3
	SLC3A2	NM_001012664.3		c.113-4182A>G		intron	N/A	NP_001012682.1	P08195-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC3A2	ENST00000377890.6	TSL:1	c.299-4182A>G		intron	N/A	ENSP00000367122.2	P08195-1
	SLC3A2	ENST00000377889.6	TSL:1	c.113-4182A>G		intron	N/A	ENSP00000367121.2	P08195-3
	SLC3A2	ENST00000538084.2	TSL:3	c.349A>G	p.Ile117Val	missense	Exon 4 of 13	ENSP00000440001.2	P08195-4

Frequencies

GnomAD3 genomes AF: 0.0000263 AC: 4 AN: 152030 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000180 AC: 1 AN: 55440 AF XY: 0.0000307

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000472

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000426 AC: 3 AN: 704910 Hom.: 0 Cov.: 9 AF XY: 0.00000575 AC XY: 2 AN XY: 347896

African (AFR) AF: 0.00 AC: 0 AN: 13024

American (AMR) AF: 0.00 AC: 0 AN: 11212

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9720

East Asian (EAS) AF: 0.00 AC: 0 AN: 3340

South Asian (SAS) AF: 0.00 AC: 0 AN: 45834

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8380

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3302

European-Non Finnish (NFE) AF: 0.00000341 AC: 2 AN: 585686

Other (OTH) AF: 0.0000410 AC: 1 AN: 24412

GnomAD4 genome AF: 0.0000263 AC: 4 AN: 152030 Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1 AN XY: 74246

African (AFR) AF: 0.0000242 AC: 1 AN: 41388

American (AMR) AF: 0.00 AC: 0 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.00 AC: 0 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10582

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68014

Other (OTH) AF: 0.00 AC: 0 AN: 2094

Alfa AF: 0.0000468 Hom.: 0

Bravo AF: 0.0000113

Asia WGS AF: 0.000289 AC: 1 AN: 3478

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	0.067
BayesDel_addAF	Benign	-0.40	T
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.21
DANN	Benign	0.43
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.020	N
LIST_S2	Benign	0.27	T
M_CAP	Benign	0.0022	T
MetaRNN	Benign	0.040	T
MetaSVM	Benign	-0.92	T
PhyloP100		-0.038
PROVEAN	Benign	0.11	N
REVEL	Benign	0.052
Sift	Benign	0.88	T
Sift4G	Benign	0.37	T
Vest4		0.17
MVP		0.082
MPC		0.41
ClinPred		0.037	T
GERP RS		0.40
gMVP		0.017
Mutation Taster		=98/2	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: rs1461175319; hg19: chr11-62644309;