rs13197601

chr6-25785707-G-A

Variant summary

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

The NM_005074.5(SLC17A1):c.*3-2489C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,818 control chromosomes in the GnomAD database, including 9,434 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 0.32 (9434 hom., cov: 32)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.649

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC17A1	NM_005074.5	c.*3-2489C>T		intron_variant		ENST00000244527.10
SLC17A1	XM_011514818.3	c.1179-2489C>T		intron_variant
SLC17A1	XM_017011201.3	c.*2+13076C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC17A1	ENST00000244527.10	c.*3-2489C>T		intron_variant		5	NM_005074.5	P1
SLC17A1	ENST00000377886.6	c.*658-2489C>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48272 AN: 151700 Hom.: 9437 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.318 AC: 48269 AN: 151818 Hom.: 9434 Cov.: 32 AF XY: 0.316 AC XY: 23464 AN XY: 74176

Gnomad4 AFR AF: 0.0999

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.322

Alfa AF: 0.365 Hom.: 1408

Bravo AF: 0.301

Asia WGS AF: 0.305 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.4
Dann	Benign	0.61

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: rs13197601; hg19: chr6-25785935;