rs17270561

chr6-25820211-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005074.5(SLC17A1):c.208-296G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,172 control chromosomes in the GnomAD database, including 3,074 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 0.18 (3074 hom., cov: 32)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

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=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC17A1	NM_005074.5	c.208-296G>T		intron_variant		ENST00000244527.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC17A1	ENST00000244527.10	c.208-296G>T		intron_variant		5	NM_005074.5	P1
SLC17A1	ENST00000468082.1	c.208-296G>T		intron_variant		1
SLC17A1	ENST00000476801.5	c.208-296G>T		intron_variant		2		P1
SLC17A1	ENST00000377886.6	c.208-296G>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26772 AN: 152052 Hom.: 3070 Cov.: 32

Gnomad AFR AF: 0.0462

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.176 AC: 26785 AN: 152172 Hom.: 3074 Cov.: 32 AF XY: 0.179 AC XY: 13346 AN XY: 74386

Gnomad4 AFR AF: 0.0461

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.159

Alfa AF: 0.210 Hom.: 5605

Bravo AF: 0.159

Asia WGS AF: 0.161 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	5.5
Dann	Benign	0.86

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: rs17270561; hg19: chr6-25820439;