chr11-62889032-T-C

Variant names:

• chr11-62889032-T-C
• rs2282477
• NM_001013251.3:c.*339T>C

Variant summary

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

The NM_001013251.3(SLC3A2):​c.*339T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,148 control chromosomes in the GnomAD database, including 3,009 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 (3009 hom., cov: 32)
• Consequence: SLC3A2 NM_001013251.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• 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 (EAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001013251.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC3A2	NM_001013251.3	MANE Select	c.*339T>C		downstream_gene	N/A	NP_001013269.1
	SLC3A2	NM_001012662.3		c.*339T>C		downstream_gene	N/A	NP_001012680.1
	SLC3A2	NM_002394.6		c.*339T>C		downstream_gene	N/A	NP_002385.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC3A2	ENST00000338663.12	TSL:1 MANE Select	c.*339T>C		downstream_gene	N/A	ENSP00000340815.7
	SLC3A2	ENST00000377890.6	TSL:1	c.*339T>C		downstream_gene	N/A	ENSP00000367122.2
	SLC3A2	ENST00000377889.6	TSL:1	c.*339T>C		downstream_gene	N/A	ENSP00000367121.2

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29858 AN: 152026 Hom.: 3009 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.196 AC: 29877 AN: 152148 Hom.: 3009 Cov.: 32 AF XY: 0.198 AC XY: 14746 AN XY: 74390

African (AFR) AF: 0.164 AC: 6809 AN: 41516

American (AMR) AF: 0.203 AC: 3102 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 766 AN: 3472

East Asian (EAS) AF: 0.254 AC: 1308 AN: 5158

South Asian (SAS) AF: 0.199 AC: 963 AN: 4830

European-Finnish (FIN) AF: 0.225 AC: 2384 AN: 10586

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13867 AN: 67984

Other (OTH) AF: 0.199 AC: 421 AN: 2112

Alfa AF: 0.202 Hom.: 8180

Bravo AF: 0.198

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.14
DANN	Benign	0.30
PhyloP100		-2.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2282477; hg19: chr11-62656504;