11-62884591-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC3A2	NM_001013251.3	c.760-41A>G		intron_variant	Intron 4 of 8	ENST00000338663.12	NP_001013269.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC3A2	ENST00000338663.12	c.760-41A>G		intron_variant	Intron 4 of 8	1	NM_001013251.3	ENSP00000340815.7

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

GnomAD3 exomes AF: 0.841 AC: 211319 AN: 251170 Hom.: 89946 AF XY: 0.853 AC XY: 115850 AN XY: 135760

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 SAS exome AF: 0.885

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

Gnomad4 AFR exome AF: 0.635

Gnomad4 AMR exome AF: 0.701

Gnomad4 ASJ exome AF: 0.792

Gnomad4 EAS exome AF: 0.829

Gnomad4 SAS exome AF: 0.884

Gnomad4 FIN exome AF: 0.880

Gnomad4 NFE exome AF: 0.903

Gnomad4 OTH exome AF: 0.872

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

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.873

Gnomad4 NFE AF: 0.899

Gnomad4 OTH AF: 0.825

Alfa AF: 0.876 Hom.: 84177

Bravo AF: 0.787

Asia WGS AF: 0.835 AC: 2907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.48
RBP_binding_hub_radar		0.67
RBP_regulation_power_radar		2.0

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: rs489381; hg19: chr11-62652063; COSMIC: COSV58605089; COSMIC: COSV58605089;