rs13199775

Positions:

• chr6-25828554-A-T

Variant summary

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

The NM_005074.5(SLC17A1):​c.35-1921T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0723 in 152,024 control chromosomes in the GnomAD database, including 438 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 0.072 (438 hom., cov: 32)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC17A1	NM_005074.5	c.35-1921T>A		intron_variant		ENST00000244527.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC17A1	ENST00000244527.10	c.35-1921T>A		intron_variant		5	NM_005074.5	P1
SLC17A1	ENST00000468082.1	c.35-1921T>A		intron_variant		1
SLC17A1	ENST00000476801.5	c.35-1921T>A		intron_variant		2		P1
SLC17A1	ENST00000377886.6	c.35-1921T>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0723 AC: 10990 AN: 151906 Hom.: 439 Cov.: 32

Gnomad AFR AF: 0.0836

Gnomad AMI AF: 0.0187

Gnomad AMR AF: 0.0524

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.0397

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0867

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0723 AC: 10986 AN: 152024 Hom.: 438 Cov.: 32 AF XY: 0.0679 AC XY: 5052 AN XY: 74362

Gnomad4 AFR AF: 0.0835

Gnomad4 AMR AF: 0.0522

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.0151

Gnomad4 SAS AF: 0.0149

Gnomad4 FIN AF: 0.0397

Gnomad4 NFE AF: 0.0867

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0819 Hom.: 66

Bravo AF: 0.0758

Asia WGS AF: 0.0200 AC: 69 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.0
DANN	Benign	0.43

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: rs13199775; hg19: chr6-25828782;