rs12794763

Variant names:

• chr11-62858040-T-G
• rs12794763
• ENST00000377890.6:c.112+1659T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000377890.6(SLC3A2):​c.112+1659T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,000 control chromosomes in the GnomAD database, including 2,437 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (2437 hom., cov: 31)
• Consequence: SLC3A2 ENST00000377890.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548
• Publications: 9 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC3A2	NM_001012662.3	c.112+1659T>G		intron_variant	Intron 1 of 11		NP_001012680.1
SLC3A2	NM_002394.6	c.112+1659T>G		intron_variant	Intron 1 of 11		NP_002385.3
SLC3A2	NM_001012664.3	c.112+1659T>G		intron_variant	Intron 1 of 9		NP_001012682.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC3A2	ENST00000377890.6	c.112+1659T>G		intron_variant	Intron 1 of 11	1		ENSP00000367122.2
SLC3A2	ENST00000377889.6	c.112+1659T>G		intron_variant	Intron 1 of 9	1		ENSP00000367121.2
SLC3A2	ENST00000538084.2	c.112+1659T>G		intron_variant	Intron 1 of 12	3		ENSP00000440001.2

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21983 AN: 151882 Hom.: 2433 Cov.: 31

Gnomad AFR AF: 0.0330

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.153

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.145 AC: 21993 AN: 152000 Hom.: 2437 Cov.: 31 AF XY: 0.156 AC XY: 11592 AN XY: 74268

African (AFR) AF: 0.0330 AC: 1369 AN: 41482

American (AMR) AF: 0.330 AC: 5036 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0784 AC: 272 AN: 3468

East Asian (EAS) AF: 0.250 AC: 1296 AN: 5174

South Asian (SAS) AF: 0.369 AC: 1774 AN: 4814

European-Finnish (FIN) AF: 0.234 AC: 2465 AN: 10534

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9349 AN: 67970

Other (OTH) AF: 0.154 AC: 325 AN: 2110

Alfa AF: 0.144 Hom.: 4113

Bravo AF: 0.145

Asia WGS AF: 0.352 AC: 1224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.4
DANN	Benign	0.26
PhyloP100		0.55
Mutation Taster		=100/0	polymorphism (auto)

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: rs12794763; hg19: chr11-62625512;