rs1165208

chr6-25803676-G-Achr6-25803676-G-T

Variant summary

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

The NM_005074.5(SLC17A1):c.1179-2696C>T 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 151,894 control chromosomes in the GnomAD database, including 11,972 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 (11972 hom., cov: 31)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.650

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC17A1	NM_005074.5	c.1179-2696C>T		intron_variant		ENST00000244527.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC17A1	ENST00000244527.10	c.1179-2696C>T		intron_variant		5	NM_005074.5	P1
SLC17A1	ENST00000468082.1	c.1017-2696C>T		intron_variant		1
SLC17A1	ENST00000476801.5	c.1179-2696C>T		intron_variant		2		P1
SLC17A1	ENST00000377886.6	c.*430-2696C>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58048 AN: 151776 Hom.: 11934 Cov.: 31

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: 0.422

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.383 AC: 58148 AN: 151894 Hom.: 11972 Cov.: 31 AF XY: 0.389 AC XY: 28891 AN XY: 74264

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.364

Alfa AF: 0.326 Hom.: 1263

Bravo AF: 0.392

Asia WGS AF: 0.514 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	8.0
Dann	Benign	0.76

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: rs1165208; hg19: chr6-25803904;