rs3799369

Variant names:

• chr6-25912406-A-G
• rs3799369
• ENST00000882947.1:c.*911T>C

Variant summary

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

The ENST00000882947.1(SLC17A2):​c.*911T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.075 in 152,244 control chromosomes in the GnomAD database, including 531 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 0.075 (531 hom., cov: 32)
• Consequence: SLC17A2 ENST00000882947.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 2 publications found

Genes affected

SLC17A2 (HGNC:10930): (solute carrier family 17 member 2) Predicted to enable sialic acid transmembrane transporter activity. Predicted to be involved in sialic acid transport. Predicted to be located in membrane. Predicted to be active in lysosome. Predicted to be integral component of 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000882947.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC17A2	ENST00000882947.1		c.*911T>C		3_prime_UTR	Exon 12 of 12	ENSP00000553006.1
	SLC17A2	ENST00000882948.1		c.*911T>C		3_prime_UTR	Exon 11 of 11	ENSP00000553007.1
	SLC17A2	ENST00000882949.1		c.*911T>C		3_prime_UTR	Exon 11 of 11	ENSP00000553008.1

Frequencies

GnomAD3 genomes AF: 0.0751 AC: 11429 AN: 152126 Hom.: 533 Cov.: 32

Gnomad AFR AF: 0.0206

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0778

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0279

Gnomad SAS AF: 0.0807

Gnomad FIN AF: 0.0945

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.0750 AC: 11420 AN: 152244 Hom.: 531 Cov.: 32 AF XY: 0.0742 AC XY: 5523 AN XY: 74438

African (AFR) AF: 0.0206 AC: 855 AN: 41554

American (AMR) AF: 0.0779 AC: 1192 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3466

East Asian (EAS) AF: 0.0276 AC: 143 AN: 5188

South Asian (SAS) AF: 0.0795 AC: 384 AN: 4828

European-Finnish (FIN) AF: 0.0945 AC: 1001 AN: 10592

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7134 AN: 67996

Other (OTH) AF: 0.0903 AC: 191 AN: 2114

Alfa AF: 0.0963 Hom.: 1497

Bravo AF: 0.0716

Asia WGS AF: 0.0660 AC: 229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.39
DANN	Benign	0.57
PhyloP100		0.14

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3799369; hg19: chr6-25912634;