rs12804553

Positions:

• chr11-62876155-G-T

Variant summary

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

The ENST00000377890.6(SLC3A2):​c.298+4486G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,244 control chromosomes in the GnomAD database, including 3,909 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 0.21 (3909 hom., cov: 33)
• Consequence: SLC3A2 ENST00000377890.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185

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 = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC3A2	NM_001012662.3	c.206-629G>T		intron_variant
SLC3A2	NM_001012664.3	c.113-4864G>T		intron_variant
SLC3A2	NM_002394.6	c.298+4486G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC3A2	ENST00000377889.6	c.113-4864G>T		intron_variant		1
SLC3A2	ENST00000377890.6	c.298+4486G>T		intron_variant		1
SLC3A2	ENST00000377891.6	c.206-629G>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31487 AN: 152126 Hom.: 3905 Cov.: 33

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.207 AC: 31484 AN: 152244 Hom.: 3909 Cov.: 33 AF XY: 0.205 AC XY: 15234 AN XY: 74426

Gnomad4 AFR AF: 0.0690

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.227

Alfa AF: 0.258 Hom.: 1297

Bravo AF: 0.194

Asia WGS AF: 0.142 AC: 494 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	0.64
DANN	Benign	0.32

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: rs12804553; hg19: chr11-62643627;