chr11-62876155-G-T

Variant names:

• chr11-62876155-G-T
• rs12804553
• ENST00000377890.6:c.298+4486G>T

Variant summary

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

The NM_001012662.3(SLC3A2):​c.206-629G>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 NM_001012662.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 5 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 = 0.291 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001012662.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC3A2	NM_001012662.3		c.206-629G>T		intron	N/A	NP_001012680.1
	SLC3A2	NM_002394.6		c.298+4486G>T		intron	N/A	NP_002385.3
	SLC3A2	NM_001012664.3		c.113-4864G>T		intron	N/A	NP_001012682.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC3A2	ENST00000377890.6	TSL:1	c.298+4486G>T		intron	N/A	ENSP00000367122.2
	SLC3A2	ENST00000377889.6	TSL:1	c.113-4864G>T		intron	N/A	ENSP00000367121.2
	SLC3A2	ENST00000538084.2	TSL:3	c.299-632G>T		intron	N/A	ENSP00000440001.2

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

African (AFR) AF: 0.0690 AC: 2869 AN: 41576

American (AMR) AF: 0.185 AC: 2832 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 751 AN: 3470

East Asian (EAS) AF: 0.121 AC: 627 AN: 5188

South Asian (SAS) AF: 0.186 AC: 898 AN: 4828

European-Finnish (FIN) AF: 0.252 AC: 2671 AN: 10594

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20042 AN: 68004

Other (OTH) AF: 0.227 AC: 479 AN: 2114

Alfa AF: 0.259 Hom.: 2093

Bravo AF: 0.194

Asia WGS AF: 0.142 AC: 494 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	0.64
DANN	Benign	0.32
PhyloP100		0.18
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: rs12804553; hg19: chr11-62643627;