chr11-62880793-C-G

Variant names:

• chr11-62880793-C-G
• rs12274689
• ENST00000377890.6:c.299-226C>G

Variant summary

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

The ENST00000377890.6(SLC3A2):​c.299-226C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00703 in 825,818 control chromosomes in the GnomAD database, including 263 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 0.026 (179 hom., cov: 32)
  • Exomes 𝑓: 0.0028 (84 hom.)
• Consequence: SLC3A2 ENST00000377890.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411
• Publications: 2 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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0878 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000377890.6. 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_001012662.3		c.302-226C>G		intron	N/A	NP_001012680.1
	SLC3A2	NM_002394.6		c.299-226C>G		intron	N/A	NP_002385.3
	SLC3A2	NM_001012664.3		c.113-226C>G		intron	N/A	NP_001012682.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC3A2	ENST00000377890.6	TSL:1	c.299-226C>G		intron	N/A	ENSP00000367122.2
	SLC3A2	ENST00000377889.6	TSL:1	c.113-226C>G		intron	N/A	ENSP00000367121.2
	SLC3A2	ENST00000538084.2	TSL:3	c.392-226C>G		intron	N/A	ENSP00000440001.2

Frequencies

GnomAD3 genomes AF: 0.0257 AC: 3909 AN: 152242 Hom.: 179 Cov.: 32

Gnomad AFR AF: 0.0903

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00681

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000411

Gnomad OTH AF: 0.0158

GnomAD4 exome AF: 0.00280 AC: 1889 AN: 673458 Hom.: 84 Cov.: 9 AF XY: 0.00231 AC XY: 781 AN XY: 338400

African (AFR) AF: 0.0925 AC: 1513 AN: 16352

American (AMR) AF: 0.00496 AC: 74 AN: 14918

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14466

East Asian (EAS) AF: 0.00 AC: 0 AN: 29598

South Asian (SAS) AF: 0.000187 AC: 8 AN: 42832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28380

Middle Eastern (MID) AF: 0.00292 AC: 7 AN: 2398

European-Non Finnish (NFE) AF: 0.000205 AC: 101 AN: 491820

Other (OTH) AF: 0.00569 AC: 186 AN: 32694

GnomAD4 genome AF: 0.0257 AC: 3919 AN: 152360 Hom.: 179 Cov.: 32 AF XY: 0.0254 AC XY: 1890 AN XY: 74510

African (AFR) AF: 0.0902 AC: 3752 AN: 41584

American (AMR) AF: 0.00680 AC: 104 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4834

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10624

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000412 AC: 28 AN: 68040

Other (OTH) AF: 0.0156 AC: 33 AN: 2114

Alfa AF: 0.0193 Hom.: 11

Bravo AF: 0.0284

Asia WGS AF: 0.00577 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.6
DANN	Benign	0.70
PhyloP100		-0.41
PromoterAI		0.011	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs12274689; hg19: chr11-62648265;