rs17671169

chr1-110181223-G-A

Variant summary

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

The NM_001010898.4(SLC6A17):c.864+4484G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,052 control chromosomes in the GnomAD database, including 10,948 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 0.34 (10948 hom., cov: 32)
• Consequence: SLC6A17 NM_001010898.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910

Genes affected

SLC6A17 (HGNC:31399): (solute carrier family 6 member 17) The protein encoded by this gene is a member of the SLC6 family of transporters, which are responsible for the presynaptic uptake of most neurotransmitters. The encoded vesicular transporter is selective for proline, glycine, leucine and alanine. In mouse, the strongest expression of this gene was in cortical and hippocampal tissues where expression increased during embryonic brain development and peaked postnatally. Defects in this gene cause a form of autosomal recessive intellectual disability. [provided by RefSeq, Jul 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A17	NM_001010898.4	c.864+4484G>A		intron_variant		ENST00000331565.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A17	ENST00000331565.5	c.864+4484G>A		intron_variant		2	NM_001010898.4	P1

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52415 AN: 151934 Hom.: 10952 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.357

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.345 AC: 52400 AN: 152052 Hom.: 10948 Cov.: 32 AF XY: 0.345 AC XY: 25655 AN XY: 74294

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.355

Alfa AF: 0.401 Hom.: 3642

Bravo AF: 0.318

Asia WGS AF: 0.267 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.1
Dann	Benign	0.32

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

LitVar

Other links and lift over

dbSNP: rs17671169; hg19: chr1-110723845;