6-25791517-A-T

Variant names:

• chr6-25791517-A-T
• rs1179086
• NM_005074.5:c.*2+7266T>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.*2+7266T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,058 control chromosomes in the GnomAD database, including 11,998 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 0.38 (11998 hom., cov: 33)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC17A1	NM_005074.5	c.*2+7266T>A		intron_variant	Intron 12 of 12	ENST00000244527.10	NP_005065.2
SLC17A1	XM_017011201.3	c.*2+7266T>A		intron_variant	Intron 12 of 12		XP_016866690.2
SLC17A1	XM_011514818.3	c.1179-8299T>A		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+7266T>A		intron_variant	Intron 12 of 12	5	NM_005074.5	ENSP00000244527.4
SLC17A1	ENST00000377886.6	n.*657+7266T>A		intron_variant	Intron 11 of 11	5		ENSP00000367118.2

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58112 AN: 151940 Hom.: 11958 Cov.: 33

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.383 AC: 58215 AN: 152058 Hom.: 11998 Cov.: 33 AF XY: 0.389 AC XY: 28923 AN XY: 74338

African (AFR) AF: 0.473 AC: 19623 AN: 41448

American (AMR) AF: 0.439 AC: 6712 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 708 AN: 3470

East Asian (EAS) AF: 0.699 AC: 3606 AN: 5162

South Asian (SAS) AF: 0.341 AC: 1644 AN: 4824

European-Finnish (FIN) AF: 0.421 AC: 4458 AN: 10582

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20371 AN: 67974

Other (OTH) AF: 0.364 AC: 769 AN: 2110

Alfa AF: 0.187 Hom.: 366

Bravo AF: 0.392

Asia WGS AF: 0.515 AC: 1790 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.60
PhyloP100		-0.16
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: rs1179086; hg19: chr6-25791745;