6-25928148-G-T

Variant names:

• chr6-25928148-G-T
• rs9295676
• NM_001286123.3:c.-84+2129C>A

Variant summary

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

The NM_001286123.3(SLC17A2):​c.-84+2129C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0914 in 151,856 control chromosomes in the GnomAD database, including 1,583 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 0.091 (1583 hom., cov: 32)
• Consequence: SLC17A2 NM_001286123.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC17A2	NM_001286123.3	c.-84+2129C>A		intron_variant	Intron 1 of 11	ENST00000377850.8	NP_001273052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC17A2	ENST00000377850.8	c.-84+2129C>A		intron_variant	Intron 1 of 11	5	NM_001286123.3	ENSP00000367081.3
SLC17A2	ENST00000360488.7	c.-84+2129C>A		intron_variant	Intron 1 of 10	1		ENSP00000353677.3

Frequencies

GnomAD3 genomes AF: 0.0913 AC: 13857 AN: 151738 Hom.: 1576 Cov.: 32

Gnomad AFR AF: 0.0804

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.0518

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0407

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.0914 AC: 13876 AN: 151856 Hom.: 1583 Cov.: 32 AF XY: 0.0990 AC XY: 7345 AN XY: 74168

African (AFR) AF: 0.0804 AC: 3331 AN: 41416

American (AMR) AF: 0.182 AC: 2774 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.0591 AC: 205 AN: 3470

East Asian (EAS) AF: 0.593 AC: 3020 AN: 5094

South Asian (SAS) AF: 0.189 AC: 911 AN: 4816

European-Finnish (FIN) AF: 0.0518 AC: 545 AN: 10528

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.0408 AC: 2771 AN: 68000

Other (OTH) AF: 0.116 AC: 245 AN: 2108

Alfa AF: 0.0662 Hom.: 4016

Bravo AF: 0.103

Asia WGS AF: 0.328 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.71
PhyloP100		-1.7
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: rs9295676; hg19: chr6-25928376;