GeneBe

ENST00000524041.1:c.1830-152C>T

Variant names:

Variant summary

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

The ENST00000524041.1(SLC6A7):​c.1830-152C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,068 control chromosomes in the GnomAD database, including 4,679 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 0.25 ( 4679 hom., cov: 32)

Consequence

SLC6A7
ENST00000524041.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.258

Publications

12 publications found
Variant links:
Genes affected
SLC6A7 (HGNC:11054): (solute carrier family 6 member 7) This gene is a member of the gamma-aminobutyric acid (GABA) neurotransmitter gene family and encodes a high-affinity mammalian brain L-proline transporter protein. This transporter protein differs from other sodium-dependent plasma membrane carriers by its pharmacological specificity, kinetic properties, and ionic requirements. [provided by RefSeq, Jul 2008]

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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 (AMR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC6A7ENST00000524041.1 linkc.1830-152C>T intron_variant Intron 14 of 15 5 ENSP00000428200.1 E5RJL1

Frequencies

GnomAD3 genomes
AF:
0.245
AC:
37286
AN:
151950
Hom.:
4680
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.212
Gnomad AMI
AF:
0.133
Gnomad AMR
AF:
0.286
Gnomad ASJ
AF:
0.173
Gnomad EAS
AF:
0.138
Gnomad SAS
AF:
0.155
Gnomad FIN
AF:
0.238
Gnomad MID
AF:
0.146
Gnomad NFE
AF:
0.278
Gnomad OTH
AF:
0.240
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.245
AC:
37298
AN:
152068
Hom.:
4679
Cov.:
32
AF XY:
0.241
AC XY:
17916
AN XY:
74344
show subpopulations
African (AFR)
AF:
0.212
AC:
8803
AN:
41476
American (AMR)
AF:
0.286
AC:
4361
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.173
AC:
600
AN:
3466
East Asian (EAS)
AF:
0.137
AC:
712
AN:
5180
South Asian (SAS)
AF:
0.155
AC:
745
AN:
4810
European-Finnish (FIN)
AF:
0.238
AC:
2519
AN:
10582
Middle Eastern (MID)
AF:
0.133
AC:
39
AN:
294
European-Non Finnish (NFE)
AF:
0.278
AC:
18900
AN:
67966
Other (OTH)
AF:
0.236
AC:
498
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1447
2894
4341
5788
7235
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
382
764
1146
1528
1910
<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:
0.254
Hom.:
9469
Bravo
AF:
0.248
Asia WGS
AF:
0.138
AC:
479
AN:
3478

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
0.78
PhyloP100
-0.26
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs980272; hg19: chr5-149596955; COSMIC: COSV107410518; COSMIC: COSV107410518; API