5-150216429-G-T

Variant summary

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

The ENST00000524041.1(SLC6A7):​c.1830-1115G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 152,098 control chromosomes in the GnomAD database, including 11,928 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 0.39 ( 11928 hom., cov: 33)

Consequence

SLC6A7
ENST00000524041.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.305
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]

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=-0.62).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC6A7ENST00000524041.1 linkuse as main transcriptc.1830-1115G>T intron_variant 5 ENSP00000428200

Frequencies

GnomAD3 genomes
AF:
0.393
AC:
59733
AN:
151980
Hom.:
11905
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.456
Gnomad AMI
AF:
0.252
Gnomad AMR
AF:
0.409
Gnomad ASJ
AF:
0.280
Gnomad EAS
AF:
0.384
Gnomad SAS
AF:
0.463
Gnomad FIN
AF:
0.338
Gnomad MID
AF:
0.392
Gnomad NFE
AF:
0.364
Gnomad OTH
AF:
0.388
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.393
AC:
59801
AN:
152098
Hom.:
11928
Cov.:
33
AF XY:
0.394
AC XY:
29264
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.456
Gnomad4 AMR
AF:
0.409
Gnomad4 ASJ
AF:
0.280
Gnomad4 EAS
AF:
0.384
Gnomad4 SAS
AF:
0.463
Gnomad4 FIN
AF:
0.338
Gnomad4 NFE
AF:
0.363
Gnomad4 OTH
AF:
0.388
Alfa
AF:
0.377
Hom.:
5104
Bravo
AF:
0.400
Asia WGS
AF:
0.432
AC:
1505
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
CADD
Benign
7.2
DANN
Benign
0.87

Splicing

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: rs887346; hg19: chr5-149595992; API