rs887346

Variant names:

• chr5-150216429-G-T
• rs887346
• ENST00000524041.1:c.1830-1115G>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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC6A7	ENST00000524041.1	c.1830-1115G>T		intron_variant	Intron 14 of 15	5		ENSP00000428200.1

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;