6-25786765-C-T

Variant names:

• chr6-25786765-C-T
• rs3799344
• NM_005074.5:c.*3-3547G>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.*3-3547G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,838 control chromosomes in the GnomAD database, including 12,706 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 0.40 (12706 hom., cov: 30)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• Publications: 18 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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC17A1	NM_005074.5	c.*3-3547G>A		intron_variant	Intron 12 of 12	ENST00000244527.10	NP_005065.2
SLC17A1	XM_017011201.3	c.*2+12018G>A		intron_variant	Intron 12 of 12		XP_016866690.2
SLC17A1	XM_011514818.3	c.1179-3547G>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.*3-3547G>A		intron_variant	Intron 12 of 12	5	NM_005074.5	ENSP00000244527.4
SLC17A1	ENST00000377886.6	n.*658-3547G>A		intron_variant	Intron 11 of 11	5		ENSP00000367118.2

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61293 AN: 151720 Hom.: 12703 Cov.: 30

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.404 AC: 61323 AN: 151838 Hom.: 12706 Cov.: 30 AF XY: 0.401 AC XY: 29752 AN XY: 74186

African (AFR) AF: 0.343 AC: 14207 AN: 41376

American (AMR) AF: 0.379 AC: 5793 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1806 AN: 3462

East Asian (EAS) AF: 0.239 AC: 1231 AN: 5154

South Asian (SAS) AF: 0.459 AC: 2209 AN: 4810

European-Finnish (FIN) AF: 0.373 AC: 3924 AN: 10516

Middle Eastern (MID) AF: 0.462 AC: 134 AN: 290

European-Non Finnish (NFE) AF: 0.450 AC: 30596 AN: 67938

Other (OTH) AF: 0.394 AC: 830 AN: 2106

Alfa AF: 0.449 Hom.: 10750

Bravo AF: 0.397

Asia WGS AF: 0.343 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.95
DANN	Benign	0.52
PhyloP100		-0.36
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: rs3799344; hg19: chr6-25786993;