rs13199775

Variant names:

• chr6-25828554-A-T
• rs13199775
• NM_005074.5:c.35-1921T>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.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
• Publications: 8 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=-0.95).
• 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 rank	MANE	Protein	UniProt
SLC17A1	NM_005074.5	c.35-1921T>A		intron_variant	Intron 2 of 12	ENST00000244527.10	NP_005065.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC17A1	ENST00000244527.10	c.35-1921T>A		intron_variant	Intron 2 of 12	5	NM_005074.5	ENSP00000244527.4
SLC17A1	ENST00000468082.1	c.35-1921T>A		intron_variant	Intron 1 of 9	1		ENSP00000420546.1
SLC17A1	ENST00000476801.5	c.35-1921T>A		intron_variant	Intron 2 of 11	2		ENSP00000420614.1
SLC17A1	ENST00000377886.6	n.35-1921T>A		intron_variant	Intron 2 of 11	5		ENSP00000367118.2

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

African (AFR) AF: 0.0835 AC: 3466 AN: 41504

American (AMR) AF: 0.0522 AC: 797 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0303 AC: 105 AN: 3468

East Asian (EAS) AF: 0.0151 AC: 78 AN: 5174

South Asian (SAS) AF: 0.0149 AC: 72 AN: 4824

European-Finnish (FIN) AF: 0.0397 AC: 418 AN: 10516

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0867 AC: 5891 AN: 67954

Other (OTH) AF: 0.0634 AC: 134 AN: 2112

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
PhyloP100		0.26
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: rs13199775; hg19: chr6-25828782;