rs17342717

Variant names:

• chr6-25821542-C-T
• rs17342717
• NM_005074.5:c.208-1627G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 43 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=-0.87).
• 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 rank	MANE	Protein	UniProt
SLC17A1	NM_005074.5	c.208-1627G>A		intron_variant	Intron 3 of 12	ENST00000244527.10	NP_005065.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC17A1	ENST00000244527.10	c.208-1627G>A		intron_variant	Intron 3 of 12	5	NM_005074.5	ENSP00000244527.4
SLC17A1	ENST00000468082.1	c.208-1627G>A		intron_variant	Intron 2 of 9	1		ENSP00000420546.1
SLC17A1	ENST00000476801.5	c.208-1627G>A		intron_variant	Intron 3 of 11	2		ENSP00000420614.1
SLC17A1	ENST00000377886.6	n.208-1627G>A		intron_variant	Intron 3 of 11	5		ENSP00000367118.2

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

African (AFR) AF: 0.0158 AC: 656 AN: 41540

American (AMR) AF: 0.0420 AC: 641 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0230 AC: 80 AN: 3472

East Asian (EAS) AF: 0.00463 AC: 24 AN: 5182

South Asian (SAS) AF: 0.0170 AC: 82 AN: 4822

European-Finnish (FIN) AF: 0.0793 AC: 841 AN: 10602

Middle Eastern (MID) AF: 0.0171 AC: 5 AN: 292

European-Non Finnish (NFE) AF: 0.0975 AC: 6625 AN: 67980

Other (OTH) AF: 0.0525 AC: 111 AN: 2116

Alfa AF: 0.0808 Hom.: 1957

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
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17342717; hg19: chr6-25821770;