rs12794763

Positions:

• chr11-62858040-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SLC3A2	NM_001012662.3	c.112+1659T>G		intron_variant
SLC3A2	NM_001012664.3	c.112+1659T>G		intron_variant
SLC3A2	NM_002394.6	c.112+1659T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC3A2	ENST00000377889.6	c.112+1659T>G		intron_variant		1
SLC3A2	ENST00000377890.6	c.112+1659T>G		intron_variant		1
SLC3A2	ENST00000377891.6	c.112+1659T>G		intron_variant		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

Gnomad4 AFR AF: 0.0330

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.0784

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.154

Alfa AF: 0.149 Hom.: 2801

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs12794763; hg19: chr11-62625512;