chr6-25784253-C-A

Variant names:

• chr6-25784253-C-A
• rs12662869
• NM_005074.5:c.*3-1035G>T

Variant summary

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

The NM_005074.5(SLC17A1):​c.*3-1035G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 151,998 control chromosomes in the GnomAD database, including 9,693 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 0.34 (9693 hom., cov: 32)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 8 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005074.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC17A1	NM_005074.5	MANE Select	c.*3-1035G>T		intron	N/A	NP_005065.2	Q14916-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC17A1	ENST00000244527.10	TSL:5 MANE Select	c.*3-1035G>T		intron	N/A	ENSP00000244527.4	Q14916-1
	SLC17A1	ENST00000867421.1		c.*3-2598G>T		intron	N/A	ENSP00000537480.1
	SLC17A1	ENST00000867423.1		c.*3-1035G>T		intron	N/A	ENSP00000537482.1

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51885 AN: 151880 Hom.: 9676 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.342 AC: 51934 AN: 151998 Hom.: 9693 Cov.: 32 AF XY: 0.351 AC XY: 26064 AN XY: 74318

African (AFR) AF: 0.318 AC: 13168 AN: 41442

American (AMR) AF: 0.405 AC: 6183 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 649 AN: 3472

East Asian (EAS) AF: 0.758 AC: 3913 AN: 5162

South Asian (SAS) AF: 0.342 AC: 1646 AN: 4810

European-Finnish (FIN) AF: 0.459 AC: 4840 AN: 10556

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20546 AN: 67966

Other (OTH) AF: 0.321 AC: 676 AN: 2108

Alfa AF: 0.317 Hom.: 3333

Bravo AF: 0.342

Asia WGS AF: 0.510 AC: 1771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.34
PhyloP100		-0.040
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: rs12662869; hg19: chr6-25784481;