rs13120371

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014331.4(SLC7A11):​c.*391T>C variant causes a 3 prime UTR 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
NM_014331.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.701
Variant links:
Genes affected
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
SLC7A11NM_014331.4 linkuse as main transcriptc.*391T>C 3_prime_UTR_variant 12/12 ENST00000280612.9 NP_055146.1 Q9UPY5
SLC7A11XM_047449957.1 linkuse as main transcriptc.*391T>C 3_prime_UTR_variant 18/18 XP_047305913.1
SLC7A11-AS1NR_038380.1 linkuse as main transcriptn.1860A>G non_coding_transcript_exon_variant 5/7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC7A11ENST00000280612.9 linkuse as main transcriptc.*391T>C 3_prime_UTR_variant 12/121 NM_014331.4 ENSP00000280612.5 Q9UPY5
SLC7A11-AS1ENST00000510767.5 linkuse as main transcriptn.1860A>G non_coding_transcript_exon_variant 5/71
SLC7A11-AS1ENST00000512786.1 linkuse as main transcriptn.584+2747A>G intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.292
AC:
44316
AN:
151928
Hom.:
7235
Cov.:
31
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.:
0
AF XY:
0.338
AC XY:
5260
AN XY:
15558
show subpopulations
Gnomad4 AFR exome
AF:
0.126
Gnomad4 AMR exome
AF:
0.375
Gnomad4 ASJ exome
AF:
0.394
Gnomad4 EAS exome
AF:
0.315
Gnomad4 SAS exome
AF:
0.362
Gnomad4 FIN exome
AF:
0.345
Gnomad4 NFE exome
AF:
0.333
Gnomad4 OTH exome
AF:
0.309
GnomAD4 genome
AF:
0.291
AC:
44310
AN:
152046
Hom.:
7228
Cov.:
31
AF XY:
0.297
AC XY:
22081
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.145
Gnomad4 AMR
AF:
0.344
Gnomad4 ASJ
AF:
0.414
Gnomad4 EAS
AF:
0.306
Gnomad4 SAS
AF:
0.380
Gnomad4 FIN
AF:
0.353
Gnomad4 NFE
AF:
0.343
Gnomad4 OTH
AF:
0.322
Alfa
AF:
0.317
Hom.:
2151
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
DANN
Benign
0.60
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs13120371; hg19: chr4-139092719; COSMIC: COSV54930136; COSMIC: COSV54930136; API