rs13120371

Variant names:

• chr4-138171565-A-G
• rs13120371
• ENST00000510767.6:n.1872A>G

Variant summary

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

The ENST00000510767.6(SLC7A11-AS1):​n.1872A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 183,130 control chromosomes in the GnomAD database, including 9,066 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 0.29 (7228 hom., cov: 31)
  • Exomes 𝑓: 0.33 (1838 hom.)
• Consequence: SLC7A11-AS1 ENST00000510767.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.701
• Publications: 12 publications found

Genes affected

SLC7A11-AS1 (HGNC:44064): (SLC7A11 antisense RNA 1)

SLC7A11 (HGNC:11059): (solute carrier family 7 member 11) This gene encodes a member of a heteromeric, sodium-independent, anionic amino acid transport system that is highly specific for cysteine and glutamate. In this system, designated Xc(-), the anionic form of cysteine is transported in exchange for glutamate. This protein has been identified as the predominant mediator of Kaposi sarcoma-associated herpesvirus fusion and entry permissiveness into cells. Also, increased expression of this gene in primary gliomas (compared to normal brain tissue) was associated with increased glutamate secretion via the XCT channels, resulting in neuronal cell death. [provided by RefSeq, Sep 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510767.6. 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
	SLC7A11	NM_014331.4	MANE Select	c.*391T>C		3_prime_UTR	Exon 12 of 12	NP_055146.1
	SLC7A11-AS1	NR_038380.1		n.1860A>G		non_coding_transcript_exon	Exon 5 of 7

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC7A11-AS1	ENST00000510767.6	TSL:1	n.1872A>G		non_coding_transcript_exon	Exon 5 of 7
	SLC7A11	ENST00000280612.9	TSL:1 MANE Select	c.*391T>C		3_prime_UTR	Exon 12 of 12	ENSP00000280612.5
	SLC7A11-AS1	ENST00000512786.1	TSL:3	n.584+2747A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44316 AN: 151928 Hom.: 7235 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.322

GnomAD4 exome AF: 0.335 AC: 10413 AN: 31084 Hom.: 1838 Cov.: 0 AF XY: 0.338 AC XY: 5260 AN XY: 15558

African (AFR) AF: 0.126 AC: 43 AN: 340

American (AMR) AF: 0.375 AC: 114 AN: 304

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 276 AN: 700

East Asian (EAS) AF: 0.315 AC: 140 AN: 444

South Asian (SAS) AF: 0.362 AC: 1050 AN: 2900

European-Finnish (FIN) AF: 0.345 AC: 872 AN: 2530

Middle Eastern (MID) AF: 0.482 AC: 82 AN: 170

European-Non Finnish (NFE) AF: 0.333 AC: 7171 AN: 21542

Other (OTH) AF: 0.309 AC: 665 AN: 2154

GnomAD4 genome AF: 0.291 AC: 44310 AN: 152046 Hom.: 7228 Cov.: 31 AF XY: 0.297 AC XY: 22081 AN XY: 74314

African (AFR) AF: 0.145 AC: 6001 AN: 41510

American (AMR) AF: 0.344 AC: 5255 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1435 AN: 3464

East Asian (EAS) AF: 0.306 AC: 1585 AN: 5174

South Asian (SAS) AF: 0.380 AC: 1834 AN: 4832

European-Finnish (FIN) AF: 0.353 AC: 3732 AN: 10564

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.343 AC: 23281 AN: 67926

Other (OTH) AF: 0.322 AC: 679 AN: 2110

Alfa AF: 0.315 Hom.: 3517

Bravo AF: 0.284

Asia WGS AF: 0.317 AC: 1100 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.1
DANN	Benign	0.60
PhyloP100		0.70
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs13120371; hg19: chr4-139092719; COSMIC: COSV54930136; COSMIC: COSV54930136;