rs12662869

Positions:

• chr6-25784253-C-A
• chr6-25784253-C-G
• chr6-25784253-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.*3-1035G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 151,998 control chromosomes in the GnomAD database, including 9,693 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 (9693 hom., cov: 32)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC17A1	NM_005074.5	c.*3-1035G>T		intron_variant		ENST00000244527.10	NP_005065.2
SLC17A1	XM_017011201.3	c.*2+14530G>T		intron_variant			XP_016866690.2
SLC17A1	XM_011514818.3	c.1179-1035G>T		intron_variant			XP_011513120.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC17A1	ENST00000244527.10	c.*3-1035G>T		intron_variant		5	NM_005074.5	ENSP00000244527.4
SLC17A1	ENST00000377886.6	n.*658-1035G>T		intron_variant		5		ENSP00000367118.2

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51885 AN: 151880 Hom.: 9676 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.342 AC: 51934 AN: 151998 Hom.: 9693 Cov.: 32 AF XY: 0.351 AC XY: 26064 AN XY: 74318

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.321

Alfa AF: 0.321 Hom.: 2226

Bravo AF: 0.342

Asia WGS AF: 0.510 AC: 1771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.34

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: rs12662869; hg19: chr6-25784481;