6-25817561-A-G

Variant summary

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

The NM_005074.5(SLC17A1):c.616+1507T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 152,076 control chromosomes in the GnomAD database, including 34,944 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 0.66 (34944 hom., cov: 32)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC17A1	NM_005074.5	c.616+1507T>C		intron_variant		ENST00000244527.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC17A1	ENST00000244527.10	c.616+1507T>C		intron_variant		5	NM_005074.5	P1
SLC17A1	ENST00000468082.1	c.616+1507T>C		intron_variant		1
SLC17A1	ENST00000476801.5	c.616+1507T>C		intron_variant		2		P1
SLC17A1	ENST00000377886.6	c.616+1507T>C		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100406 AN: 151958 Hom.: 34885 Cov.: 32

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.661 AC: 100526 AN: 152076 Hom.: 34944 Cov.: 32 AF XY: 0.663 AC XY: 49253 AN XY: 74334

Gnomad4 AFR AF: 0.871

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.660

Alfa AF: 0.507 Hom.: 5546

Bravo AF: 0.678

Asia WGS AF: 0.674 AC: 2346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	3.5
Dann	Benign	0.54

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: rs1165153; hg19: chr6-25817789;