rs887346

chr5-150216429-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

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]

ACMG classification

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	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A7	ENST00000524041.1	c.1830-1115G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59733 AN: 151980 Hom.: 11905 Cov.: 33

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

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

Other links and lift over

dbSNP: rs887346; hg19: chr5-149595992;