rs3757131

Variant names:

• chr6-25783681-C-T
• rs3757131
• NM_005074.5:c.*3-463G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005074.5(SLC17A1):​c.*3-463G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,018 control chromosomes in the GnomAD database, including 9,536 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 0.32 (9536 hom., cov: 31)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC17A1	NM_005074.5	c.*3-463G>A		intron_variant	Intron 12 of 12	ENST00000244527.10	NP_005065.2
SLC17A1	XM_017011201.3	c.*2+15102G>A		intron_variant	Intron 12 of 12		XP_016866690.2
SLC17A1	XM_011514818.3	c.1179-463G>A		intron_variant	Intron 10 of 10		XP_011513120.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC17A1	ENST00000244527.10	c.*3-463G>A		intron_variant	Intron 12 of 12	5	NM_005074.5	ENSP00000244527.4
SLC17A1	ENST00000377886.6	n.*658-463G>A		intron_variant	Intron 11 of 11	5		ENSP00000367118.2

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48572 AN: 151900 Hom.: 9539 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.320 AC: 48570 AN: 152018 Hom.: 9536 Cov.: 31 AF XY: 0.318 AC XY: 23611 AN XY: 74286

African (AFR) AF: 0.103 AC: 4265 AN: 41492

American (AMR) AF: 0.328 AC: 5008 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1768 AN: 3470

East Asian (EAS) AF: 0.160 AC: 827 AN: 5174

South Asian (SAS) AF: 0.450 AC: 2165 AN: 4814

European-Finnish (FIN) AF: 0.339 AC: 3567 AN: 10528

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29570 AN: 67962

Other (OTH) AF: 0.324 AC: 684 AN: 2114

Alfa AF: 0.393 Hom.: 4158

Bravo AF: 0.303

Asia WGS AF: 0.306 AC: 1063 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.65
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3757131; hg19: chr6-25783909;