rs1127773

Variant summary

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

The ENST00000379152.7(SLC7A6):​n.*1215G>A 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 0.503 in 152,432 control chromosomes in the GnomAD database, including 20,187 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 0.50 ( 20141 hom., cov: 32)
Exomes 𝑓: 0.52 ( 46 hom. )

Consequence

SLC7A6
ENST00000379152.7 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.31

Publications

13 publications found
Variant links:
Genes affected
SLC7A6 (HGNC:11064): (solute carrier family 7 member 6) Enables basic amino acid transmembrane transporter activity. Involved in basic amino acid transmembrane transport and ornithine transport. Located in intracellular membrane-bounded organelle and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
SLC7A6OS (HGNC:25807): (solute carrier family 7 member 6 opposite strand) Predicted to be involved in developmental process. Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be located in cytoplasm and nucleus. Implicated in progressive myoclonus epilepsy. [provided by Alliance of Genome Resources, Apr 2022]
SLC7A6OS Gene-Disease associations (from GenCC):
  • epilepsy
    Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
  • epilepsy, progressive myoclonic, 12
    Inheritance: AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

Genome browser will be placed here

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=-0.81).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC7A6NM_003983.6 linkc.*1516G>A 3_prime_UTR_variant Exon 11 of 11 ENST00000219343.11 NP_003974.3 Q92536A0A024R719
SLC7A6OSNM_032178.3 linkc.*2431C>T 3_prime_UTR_variant Exon 5 of 5 ENST00000263997.11 NP_115554.2 Q96CW6
SLC7A6NM_001076785.3 linkc.*1516G>A 3_prime_UTR_variant Exon 12 of 12 NP_001070253.1 Q92536A0A024R719

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC7A6ENST00000219343.11 linkc.*1516G>A 3_prime_UTR_variant Exon 11 of 11 1 NM_003983.6 ENSP00000219343.6 Q92536
SLC7A6OSENST00000263997.11 linkc.*2431C>T 3_prime_UTR_variant Exon 5 of 5 1 NM_032178.3 ENSP00000263997.5 Q96CW6

Frequencies

GnomAD3 genomes
AF:
0.503
AC:
76414
AN:
151912
Hom.:
20131
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.371
Gnomad AMI
AF:
0.455
Gnomad AMR
AF:
0.591
Gnomad ASJ
AF:
0.466
Gnomad EAS
AF:
0.807
Gnomad SAS
AF:
0.417
Gnomad FIN
AF:
0.479
Gnomad MID
AF:
0.326
Gnomad NFE
AF:
0.553
Gnomad OTH
AF:
0.515
GnomAD4 exome
AF:
0.520
AC:
209
AN:
402
Hom.:
46
Cov.:
0
AF XY:
0.523
AC XY:
137
AN XY:
262
show subpopulations
African (AFR)
AF:
0.500
AC:
1
AN:
2
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
1.00
AC:
4
AN:
4
South Asian (SAS)
AF:
0.500
AC:
1
AN:
2
European-Finnish (FIN)
AF:
0.506
AC:
156
AN:
308
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.551
AC:
43
AN:
78
Other (OTH)
AF:
0.500
AC:
4
AN:
8
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.516
Heterozygous variant carriers
0
5
10
15
20
25
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.503
AC:
76458
AN:
152030
Hom.:
20141
Cov.:
32
AF XY:
0.501
AC XY:
37192
AN XY:
74296
show subpopulations
African (AFR)
AF:
0.371
AC:
15365
AN:
41462
American (AMR)
AF:
0.592
AC:
9036
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
0.466
AC:
1618
AN:
3470
East Asian (EAS)
AF:
0.807
AC:
4170
AN:
5168
South Asian (SAS)
AF:
0.419
AC:
2018
AN:
4818
European-Finnish (FIN)
AF:
0.479
AC:
5061
AN:
10568
Middle Eastern (MID)
AF:
0.337
AC:
99
AN:
294
European-Non Finnish (NFE)
AF:
0.553
AC:
37606
AN:
67962
Other (OTH)
AF:
0.509
AC:
1071
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1860
3720
5579
7439
9299
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
674
1348
2022
2696
3370
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.532
Hom.:
40354
Bravo
AF:
0.511
Asia WGS
AF:
0.510
AC:
1773
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
8.3
DANN
Benign
0.54
PhyloP100
1.3
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
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

Publications

Other links and lift over

dbSNP: rs1127773; hg19: chr16-68332747; COSMIC: COSV50450879; COSMIC: COSV50450879; API