chr14-22788107-A-G

Variant summary

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

The NM_003982.4(SLC7A7):​c.500-8056T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,074 control chromosomes in the GnomAD database, including 7,898 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 0.31 ( 7898 hom., cov: 32)

Consequence

SLC7A7
NM_003982.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.51

Publications

3 publications found
Variant links:
Genes affected
SLC7A7 (HGNC:11065): (solute carrier family 7 member 7) The protein encoded by this gene is the light subunit of a cationic amino acid transporter. This sodium-independent transporter is formed when the light subunit encoded by this gene dimerizes with the heavy subunit transporter protein SLC3A2. This transporter is found in epithelial cell membranes where it transfers cationic and large neutral amino acids from the cell to the extracellular space. Defects in this gene are a cause of lysinuric protein intolerance (LPI). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2011]
SLC7A7 Gene-Disease associations (from GenCC):
  • lysinuric protein intolerance
    Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: PanelApp Australia, Orphanet, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics

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=-1.04).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC7A7NM_003982.4 linkc.500-8056T>C intron_variant Intron 2 of 9 ENST00000674313.1 NP_003973.3
SLC7A7NM_001126105.3 linkc.500-8056T>C intron_variant Intron 3 of 10 NP_001119577.1 Q9UM01A0A0S2Z502
SLC7A7NM_001126106.4 linkc.500-8056T>C intron_variant Intron 3 of 10 NP_001119578.1 Q9UM01A0A0S2Z502
SLC7A7XM_011537299.2 linkc.500-8056T>C intron_variant Intron 2 of 9 XP_011535601.1 Q9UM01A0A0S2Z502

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC7A7ENST00000674313.1 linkc.500-8056T>C intron_variant Intron 2 of 9 NM_003982.4 ENSP00000501493.1 Q9UM01

Frequencies

GnomAD3 genomes
AF:
0.307
AC:
46581
AN:
151954
Hom.:
7865
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.403
Gnomad AMI
AF:
0.223
Gnomad AMR
AF:
0.374
Gnomad ASJ
AF:
0.199
Gnomad EAS
AF:
0.599
Gnomad SAS
AF:
0.290
Gnomad FIN
AF:
0.233
Gnomad MID
AF:
0.304
Gnomad NFE
AF:
0.230
Gnomad OTH
AF:
0.308
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.307
AC:
46671
AN:
152074
Hom.:
7898
Cov.:
32
AF XY:
0.309
AC XY:
23000
AN XY:
74340
show subpopulations
African (AFR)
AF:
0.403
AC:
16721
AN:
41454
American (AMR)
AF:
0.375
AC:
5726
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
0.199
AC:
692
AN:
3470
East Asian (EAS)
AF:
0.600
AC:
3101
AN:
5170
South Asian (SAS)
AF:
0.290
AC:
1398
AN:
4824
European-Finnish (FIN)
AF:
0.233
AC:
2469
AN:
10586
Middle Eastern (MID)
AF:
0.293
AC:
86
AN:
294
European-Non Finnish (NFE)
AF:
0.230
AC:
15614
AN:
67986
Other (OTH)
AF:
0.314
AC:
661
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1608
3216
4824
6432
8040
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
460
920
1380
1840
2300
<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:
0.257
Hom.:
8811
Bravo
AF:
0.327
Asia WGS
AF:
0.440
AC:
1530
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.64
DANN
Benign
0.18
PhyloP100
-2.5
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: rs12436190; hg19: chr14-23257316; API