6-25794203-A-G

Variant names:

• chr6-25794203-A-G
• rs2762353
• NM_005074.5:c.*2+4580T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005074.5(SLC17A1):​c.*2+4580T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,088 control chromosomes in the GnomAD database, including 35,035 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 (35035 hom., cov: 31)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 27 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=-1.02).
• 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 rank	MANE	Protein	UniProt
SLC17A1	NM_005074.5	c.*2+4580T>C		intron_variant	Intron 12 of 12	ENST00000244527.10	NP_005065.2
SLC17A1	XM_017011201.3	c.*2+4580T>C		intron_variant	Intron 12 of 12		XP_016866690.2
SLC17A1	XM_011514818.3	c.1179-10985T>C		intron_variant	Intron 10 of 10		XP_011513120.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC17A1	ENST00000244527.10	c.*2+4580T>C		intron_variant	Intron 12 of 12	5	NM_005074.5	ENSP00000244527.4
SLC17A1	ENST00000377886.6	n.*657+4580T>C		intron_variant	Intron 11 of 11	5		ENSP00000367118.2

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100505 AN: 151970 Hom.: 34974 Cov.: 31

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.662 AC: 100627 AN: 152088 Hom.: 35035 Cov.: 31 AF XY: 0.663 AC XY: 49300 AN XY: 74344

African (AFR) AF: 0.873 AC: 36254 AN: 41514

American (AMR) AF: 0.655 AC: 10004 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1592 AN: 3470

East Asian (EAS) AF: 0.831 AC: 4293 AN: 5166

South Asian (SAS) AF: 0.530 AC: 2560 AN: 4826

European-Finnish (FIN) AF: 0.642 AC: 6781 AN: 10562

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37278 AN: 67968

Other (OTH) AF: 0.660 AC: 1392 AN: 2108

Alfa AF: 0.584 Hom.: 113374

Bravo AF: 0.678

Asia WGS AF: 0.677 AC: 2357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.60
PhyloP100		-1.3
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: rs2762353; hg19: chr6-25794431;