chr11-62884591-A-G

Variant names:

• chr11-62884591-A-G
• rs489381
• NM_001013251.3:c.760-41A>G

Variant summary

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

The NM_001013251.3(SLC3A2):​c.760-41A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 1,613,272 control chromosomes in the GnomAD database, including 622,349 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 0.80 (49999 hom., cov: 29)
  • Exomes 𝑓: 0.88 (572350 hom.)
• Consequence: SLC3A2 NM_001013251.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.851
• Publications: 25 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.893 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.760-41A>G		intron	N/A	NP_001013269.1
	SLC3A2	NM_001012662.3		c.1066-41A>G		intron	N/A	NP_001012680.1
	SLC3A2	NM_002394.6		c.1063-41A>G		intron	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.760-41A>G		intron	N/A	ENSP00000340815.7
	SLC3A2	ENST00000377890.6	TSL:1	c.1063-41A>G		intron	N/A	ENSP00000367122.2
	SLC3A2	ENST00000377889.6	TSL:1	c.877-41A>G		intron	N/A	ENSP00000367121.2

Frequencies

GnomAD3 genomes AF: 0.803 AC: 121976 AN: 151898 Hom.: 49979 Cov.: 29

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.829

GnomAD2 exomes AF: 0.841 AC: 211319 AN: 251170 AF XY: 0.853

Gnomad AFR exome AF: 0.632

Gnomad AMR exome AF: 0.703

Gnomad ASJ exome AF: 0.793

Gnomad EAS exome AF: 0.831

Gnomad FIN exome AF: 0.873

Gnomad NFE exome AF: 0.901

Gnomad OTH exome AF: 0.857

GnomAD4 exome AF: 0.883 AC: 1290539 AN: 1461256 Hom.: 572350 Cov.: 39 AF XY: 0.884 AC XY: 642868 AN XY: 726904

African (AFR) AF: 0.635 AC: 21256 AN: 33454

American (AMR) AF: 0.701 AC: 31308 AN: 44670

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 20683 AN: 26122

East Asian (EAS) AF: 0.829 AC: 32915 AN: 39684

South Asian (SAS) AF: 0.884 AC: 76249 AN: 86228

European-Finnish (FIN) AF: 0.880 AC: 46987 AN: 53416

Middle Eastern (MID) AF: 0.871 AC: 5023 AN: 5768

European-Non Finnish (NFE) AF: 0.903 AC: 1003469 AN: 1111540

Other (OTH) AF: 0.872 AC: 52649 AN: 60374

GnomAD4 genome AF: 0.803 AC: 122042 AN: 152016 Hom.: 49999 Cov.: 29 AF XY: 0.801 AC XY: 59513 AN XY: 74316

African (AFR) AF: 0.640 AC: 26510 AN: 41422

American (AMR) AF: 0.729 AC: 11120 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2768 AN: 3466

East Asian (EAS) AF: 0.836 AC: 4325 AN: 5174

South Asian (SAS) AF: 0.870 AC: 4196 AN: 4822

European-Finnish (FIN) AF: 0.873 AC: 9214 AN: 10560

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61117 AN: 67994

Other (OTH) AF: 0.825 AC: 1741 AN: 2110

Alfa AF: 0.868 Hom.: 124168

Bravo AF: 0.787

Asia WGS AF: 0.835 AC: 2907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.48
PhyloP100		-0.85
RBP_binding_hub_radar		0.67
RBP_regulation_power_radar		2.0
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: rs489381; hg19: chr11-62652063; COSMIC: COSV58605089; COSMIC: COSV58605089;