chr6-25791517-A-T

Position:

• chr6-25791517-A-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+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

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=-0.93).
• 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/exons	MANE	Protein	UniProt
SLC17A1	NM_005074.5	c.*2+7266T>A		intron_variant		ENST00000244527.10	NP_005065.2
SLC17A1	XM_017011201.3	c.*2+7266T>A		intron_variant			XP_016866690.2
SLC17A1	XM_011514818.3	c.1179-8299T>A		intron_variant			XP_011513120.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC17A1	ENST00000244527.10	c.*2+7266T>A		intron_variant		5	NM_005074.5	ENSP00000244527.4
SLC17A1	ENST00000377886.6	n.*657+7266T>A		intron_variant		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

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.364

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

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: rs1179086; hg19: chr6-25791745;