rs2070870

Positions:

• chr11-62881570-T-C
• chr11-62881570-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000338663.12(SLC3A2):​c.424+123T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 1,299,680 control chromosomes in the GnomAD database, including 49,802 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 0.20 (3807 hom., cov: 29)
  • Exomes 𝑓: 0.28 (45995 hom.)
• Consequence: SLC3A2 ENST00000338663.12 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.841

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC3A2	NM_001013251.3	c.424+123T>C		intron_variant		ENST00000338663.12	NP_001013269.1
SLC3A2	NM_001012662.3	c.730+123T>C		intron_variant			NP_001012680.1
SLC3A2	NM_001012664.3	c.541+123T>C		intron_variant			NP_001012682.1
SLC3A2	NM_002394.6	c.727+123T>C		intron_variant			NP_002385.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC3A2	ENST00000338663.12	c.424+123T>C		intron_variant		1	NM_001013251.3	ENSP00000340815	P2

Frequencies

GnomAD3 genomes AF: 0.205 AC: 30623 AN: 149686 Hom.: 3804 Cov.: 29

Gnomad AFR AF: 0.0677

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.225

GnomAD4 exome AF: 0.277 AC: 318233 AN: 1149878 Hom.: 45995 Cov.: 17 AF XY: 0.274 AC XY: 153727 AN XY: 560512

Gnomad4 AFR exome AF: 0.0612

Gnomad4 AMR exome AF: 0.168

Gnomad4 ASJ exome AF: 0.216

Gnomad4 EAS exome AF: 0.159

Gnomad4 SAS exome AF: 0.191

Gnomad4 FIN exome AF: 0.270

Gnomad4 NFE exome AF: 0.298

Gnomad4 OTH exome AF: 0.256

GnomAD4 genome AF: 0.204 AC: 30619 AN: 149802 Hom.: 3807 Cov.: 29 AF XY: 0.202 AC XY: 14731 AN XY: 73048

Gnomad4 AFR AF: 0.0674

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.223

Alfa AF: 0.271 Hom.: 11791

Bravo AF: 0.194

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.5
DANN	Benign	0.51

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: rs2070870; hg19: chr11-62649042;