rs13197601

Variant names:

• chr6-25785707-G-A
• rs13197601
• NM_005074.5:c.*3-2489C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC17A1	NM_005074.5	c.*3-2489C>T		intron_variant	Intron 12 of 12	ENST00000244527.10	NP_005065.2
SLC17A1	XM_017011201.3	c.*2+13076C>T		intron_variant	Intron 12 of 12		XP_016866690.2
SLC17A1	XM_011514818.3	c.1179-2489C>T		intron_variant	Intron 10 of 10		XP_011513120.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC17A1	ENST00000244527.10	c.*3-2489C>T		intron_variant	Intron 12 of 12	5	NM_005074.5	ENSP00000244527.4
SLC17A1	ENST00000377886.6	n.*658-2489C>T		intron_variant	Intron 11 of 11	5		ENSP00000367118.2

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

African (AFR) AF: 0.0999 AC: 4141 AN: 41460

American (AMR) AF: 0.327 AC: 4988 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1759 AN: 3462

East Asian (EAS) AF: 0.159 AC: 822 AN: 5170

South Asian (SAS) AF: 0.449 AC: 2159 AN: 4810

European-Finnish (FIN) AF: 0.337 AC: 3543 AN: 10512

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.434 AC: 29470 AN: 67854

Other (OTH) AF: 0.322 AC: 677 AN: 2104

Alfa AF: 0.355 Hom.: 1411

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
PhyloP100		0.65
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13197601; hg19: chr6-25785935;