rs9461216

chr6-25808515-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.1178+2883T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0682 in 151,810 control chromosomes in the GnomAD database, including 384 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 0.068 (384 hom., cov: 32)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28

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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC17A1	NM_005074.5	c.1178+2883T>A		intron_variant		ENST00000244527.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC17A1	ENST00000244527.10	c.1178+2883T>A		intron_variant		5	NM_005074.5	P1
SLC17A1	ENST00000468082.1	c.1016+2883T>A		intron_variant		1
SLC17A1	ENST00000476801.5	c.1178+2883T>A		intron_variant		2		P1
SLC17A1	ENST00000377886.6	c.*429+2883T>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0683 AC: 10362 AN: 151692 Hom.: 385 Cov.: 32

Gnomad AFR AF: 0.0683

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0512

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.0160

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.0395

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0867

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0682 AC: 10360 AN: 151810 Hom.: 384 Cov.: 32 AF XY: 0.0644 AC XY: 4784 AN XY: 74246

Gnomad4 AFR AF: 0.0683

Gnomad4 AMR AF: 0.0510

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.0160

Gnomad4 SAS AF: 0.0253

Gnomad4 FIN AF: 0.0395

Gnomad4 NFE AF: 0.0867

Gnomad4 OTH AF: 0.0578

Alfa AF: 0.0799 Hom.: 64

Bravo AF: 0.0704

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.027
Dann	Benign	0.10

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: rs9461216; hg19: chr6-25808743;