6-25791126-C-T

Position:

• chr6-25791126-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.*2+7657G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 151,978 control chromosomes in the GnomAD database, including 6,376 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 0.28 (6376 hom., cov: 32)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.815

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC17A1	NM_005074.5	c.*2+7657G>A		intron_variant		ENST00000244527.10
SLC17A1	XM_011514818.3	c.1179-7908G>A		intron_variant
SLC17A1	XM_017011201.3	c.*2+7657G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC17A1	ENST00000244527.10	c.*2+7657G>A		intron_variant		5	NM_005074.5	P1
SLC17A1	ENST00000377886.6	c.*657+7657G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42242 AN: 151860 Hom.: 6365 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.278 AC: 42261 AN: 151978 Hom.: 6376 Cov.: 32 AF XY: 0.274 AC XY: 20320 AN XY: 74296

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.295

Alfa AF: 0.266 Hom.: 841

Bravo AF: 0.286

Asia WGS AF: 0.161 AC: 561 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.19

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: rs3799346; hg19: chr6-25791354;