rs17342717

Positions:

• chr6-25821542-C-T

Variant summary

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

The NM_005074.5(SLC17A1):​c.208-1627G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0601 in 152,190 control chromosomes in the GnomAD database, including 400 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 0.060 (400 hom., cov: 32)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168

Genes affected

SLC17A1 (HGNC:10929): (solute carrier family 17 member 1) Predicted to enable sialic acid transmembrane transporter activity. Involved in urate metabolic process and urate transport. Located in apical plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC17A1	NM_005074.5	c.208-1627G>A		intron_variant		ENST00000244527.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC17A1	ENST00000244527.10	c.208-1627G>A		intron_variant		5	NM_005074.5	P1
SLC17A1	ENST00000468082.1	c.208-1627G>A		intron_variant		1
SLC17A1	ENST00000476801.5	c.208-1627G>A		intron_variant		2		P1
SLC17A1	ENST00000377886.6	c.208-1627G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0602 AC: 9148 AN: 152072 Hom.: 400 Cov.: 32

Gnomad AFR AF: 0.0158

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.0420

Gnomad ASJ AF: 0.0230

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0793

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0601 AC: 9146 AN: 152190 Hom.: 400 Cov.: 32 AF XY: 0.0561 AC XY: 4177 AN XY: 74412

Gnomad4 AFR AF: 0.0158

Gnomad4 AMR AF: 0.0420

Gnomad4 ASJ AF: 0.0230

Gnomad4 EAS AF: 0.00463

Gnomad4 SAS AF: 0.0170

Gnomad4 FIN AF: 0.0793

Gnomad4 NFE AF: 0.0975

Gnomad4 OTH AF: 0.0525

Alfa AF: 0.0843 Hom.: 916

Bravo AF: 0.0548

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.16

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs17342717; hg19: chr6-25821770;