dbSNP rs13120371: SLC7A11-AS1:n.1872A>G (chr4-138171565-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.701

Publications

12 publications found

Variant links:

Genes affected

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

SLC7A11-AS1 links:

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]

SLC7A11 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC7A11	NM_014331.4 link	c.*391T>C		3_prime_UTR_variant	Exon 12 of 12	ENST00000280612.9	NP_055146.1	Q9UPY5
SLC7A11-AS1	NR_038380.1 link	n.1860A>G		non_coding_transcript_exon_variant	Exon 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC7A11	ENST00000280612.9 link	c.*391T>C		3_prime_UTR_variant	Exon 12 of 12	1	NM_014331.4	ENSP00000280612.5		Q9UPY5

Frequencies

GnomAD3 genomes

AF:

0.292

AC:

44316

AN:

151928

Hom.:

7235

Cov.:

show subpopulations

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.:

AF XY:

0.338

AC XY:

5260

AN XY:

15558

show subpopulations

African (AFR)

AF:

0.126

AC:

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:

AN:

170

European-Non Finnish (NFE)

AF:

0.333

AC:

7171

AN:

21542

Other (OTH)

AF:

0.309

AC:

665

AN:

2154

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

348

696

1044

1392

1740

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.291

AC:

44310

AN:

152046

Hom.:

7228

Cov.:

AF XY:

0.297

AC XY:

22081

AN XY:

74314

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1578

3156

4734

6312

7890

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.1

(source)

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)

(source)

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

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rs13120371

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over