6-25786765-C-T

Position:

• chr6-25786765-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.97).
• 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/exons	MANE	UniProt
SLC17A1	NM_005074.5	c.*3-3547G>A		intron_variant		ENST00000244527.10
SLC17A1	XM_011514818.3	c.1179-3547G>A		intron_variant
SLC17A1	XM_017011201.3	c.*2+12018G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC17A1	ENST00000244527.10	c.*3-3547G>A		intron_variant		5	NM_005074.5	P1
SLC17A1	ENST00000377886.6	c.*658-3547G>A		intron_variant, NMD_transcript_variant		5

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

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.394

Alfa AF: 0.449 Hom.: 9940

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

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: rs3799344; hg19: chr6-25786993;