rs1165209

chr6-25801091-G-Achr6-25801091-G-T

Variant summary

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

The NM_005074.5(SLC17A1):c.1179-111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 659,366 control chromosomes in the GnomAD database, including 125,279 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 0.66 (35052 hom., cov: 33)
  • Exomes 𝑓: 0.59 (90227 hom.)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC17A1	NM_005074.5	c.1179-111C>T		intron_variant		ENST00000244527.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC17A1	ENST00000244527.10	c.1179-111C>T		intron_variant		5	NM_005074.5	P1
SLC17A1	ENST00000468082.1	c.1017-111C>T		intron_variant		1
SLC17A1	ENST00000476801.5	c.1179-111C>T		intron_variant		2		P1
SLC17A1	ENST00000377886.6	c.*430-111C>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100544 AN: 151998 Hom.: 34991 Cov.: 33

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.661

GnomAD4 exome AF: 0.586 AC: 297291 AN: 507250 Hom.: 90227 AF XY: 0.580 AC XY: 156911 AN XY: 270758

Gnomad4 AFR exome AF: 0.882

Gnomad4 AMR exome AF: 0.698

Gnomad4 ASJ exome AF: 0.480

Gnomad4 EAS exome AF: 0.845

Gnomad4 SAS exome AF: 0.531

Gnomad4 FIN exome AF: 0.625

Gnomad4 NFE exome AF: 0.545

Gnomad4 OTH exome AF: 0.597

GnomAD4 genome AF: 0.662 AC: 100666 AN: 152116 Hom.: 35052 Cov.: 33 AF XY: 0.663 AC XY: 49329 AN XY: 74356

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.661

Alfa AF: 0.579 Hom.: 3767

Bravo AF: 0.678

Asia WGS AF: 0.680 AC: 2368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.083
Dann	Benign	0.62

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: rs1165209; hg19: chr6-25801319;