rs3734523

Positions:

• chr6-25925759-G-A

Variant summary

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

The NM_001286123.3(SLC17A2):​c.28+10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 1,612,500 control chromosomes in the GnomAD database, including 9,306 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 0.11 (1024 hom., cov: 32)
  • Exomes 𝑓: 0.10 (8282 hom.)
• Consequence: SLC17A2 NM_001286123.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC17A2	NM_001286123.3	c.28+10C>T		intron_variant		ENST00000377850.8	NP_001273052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC17A2	ENST00000377850.8	c.28+10C>T		intron_variant		5	NM_001286123.3	ENSP00000367081	P1
SLC17A2	ENST00000360488.7	c.28+10C>T		intron_variant		1		ENSP00000353677
SLC17A2	ENST00000265425.3	c.28+10C>T		intron_variant		5		ENSP00000265425

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16037 AN: 152114 Hom.: 1023 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0750

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.0290

Gnomad FIN AF: 0.0474

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0982

Gnomad OTH AF: 0.100

GnomAD3 exomes AF: 0.0750 AC: 18852 AN: 251480 Hom.: 938 AF XY: 0.0733 AC XY: 9962 AN XY: 135910

Gnomad AFR exome AF: 0.174

Gnomad AMR exome AF: 0.0476

Gnomad ASJ exome AF: 0.0367

Gnomad EAS exome AF: 0.0175

Gnomad SAS exome AF: 0.0392

Gnomad FIN exome AF: 0.0465

Gnomad NFE exome AF: 0.0966

Gnomad OTH exome AF: 0.0789

GnomAD4 exome AF: 0.100 AC: 146360 AN: 1460268 Hom.: 8282 Cov.: 30 AF XY: 0.0973 AC XY: 70688 AN XY: 726584

Gnomad4 AFR exome AF: 0.176

Gnomad4 AMR exome AF: 0.0501

Gnomad4 ASJ exome AF: 0.0381

Gnomad4 EAS exome AF: 0.00914

Gnomad4 SAS exome AF: 0.0396

Gnomad4 FIN exome AF: 0.0476

Gnomad4 NFE exome AF: 0.113

Gnomad4 OTH exome AF: 0.0909

GnomAD4 genome AF: 0.105 AC: 16044 AN: 152232 Hom.: 1024 Cov.: 32 AF XY: 0.0996 AC XY: 7412 AN XY: 74438

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0749

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.0185

Gnomad4 SAS AF: 0.0290

Gnomad4 FIN AF: 0.0474

Gnomad4 NFE AF: 0.0981

Gnomad4 OTH AF: 0.0989

Alfa AF: 0.0953 Hom.: 1129

Bravo AF: 0.112

Asia WGS AF: 0.0380 AC: 132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.8
DANN	Benign	0.59

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: rs3734523; hg19: chr6-25925987;