Variant rs2071299 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001286123.3(SLC17A2):c.1302+7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 1,580,674 control chromosomes in the GnomAD database, including 127,350 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 0.35 ( 10394 hom., cov: 31)

Exomes 𝑓: 0.40 ( 116956 hom. )

Consequence

SLC17A2
NM_001286123.3 splice_region, intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10

Variant links:

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]

SLC17A2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC17A2	NM_001286123.3 linkuse as main transcript	c.1302+7C>T		splice_region_variant, intron_variant		ENST00000377850.8	NP_001273052.1	O00624-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SLC17A2	ENST00000377850.8 linkuse as main transcript	c.1302+7C>T		splice_region_variant, intron_variant		5	NM_001286123.3	ENSP00000367081.3	O00624-3
SLC17A2	ENST00000360488.7 linkuse as main transcript	c.1154+7C>T		splice_region_variant, intron_variant		1		ENSP00000353677.3	O00624-2
SLC17A2	ENST00000265425.3 linkuse as main transcript	c.1309C>T	p.Pro437Ser	missense_variant	10/11	5		ENSP00000265425.3	O00624-1

Frequencies

GnomAD3 genomes

AF:

0.349

AC:

53030

AN:

151776

Hom.:

10388

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.453

Gnomad AMR

AF:

0.411

Gnomad ASJ

AF:

0.360

Gnomad EAS

AF:

0.697

Gnomad SAS

AF:

0.418

Gnomad FIN

AF:

0.420

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.394

Gnomad OTH

AF:

0.369

GnomAD3 exomes

AF:

0.416

AC:

104115

AN:

250374

Hom.:

23245

AF XY:

0.413

AC XY:

55881

AN XY:

135330

show subpopulations

Gnomad AFR exome

AF:

0.176

Gnomad AMR exome

AF:

0.492

Gnomad ASJ exome

AF:

0.369

Gnomad EAS exome

AF:

0.709

Gnomad SAS exome

AF:

0.401

Gnomad FIN exome

AF:

0.412

Gnomad NFE exome

AF:

0.390

Gnomad OTH exome

AF:

0.391

GnomAD4 exome

AF:

0.397

AC:

566615

AN:

1428778

Hom.:

116956

Cov.:

AF XY:

0.397

AC XY:

283129

AN XY:

712606

show subpopulations

Gnomad4 AFR exome

AF:

0.171

Gnomad4 AMR exome

AF:

0.480

Gnomad4 ASJ exome

AF:

0.376

Gnomad4 EAS exome

AF:

0.702

Gnomad4 SAS exome

AF:

0.403

Gnomad4 FIN exome

AF:

0.414

Gnomad4 NFE exome

AF:

0.388

Gnomad4 OTH exome

AF:

0.402

GnomAD4 genome

AF:

0.349

AC:

53051

AN:

151896

Hom.:

10394

Cov.:

AF XY:

0.355

AC XY:

26370

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.180

Gnomad4 AMR

AF:

0.412

Gnomad4 ASJ

AF:

0.360

Gnomad4 EAS

AF:

0.697

Gnomad4 SAS

AF:

0.417

Gnomad4 FIN

AF:

0.420

Gnomad4 NFE

AF:

0.394

Gnomad4 OTH

AF:

0.372

Alfa

AF:

0.379

Hom.:

14989

Bravo

AF:

0.344

TwinsUK

AF:

0.377

AC:

1397

ALSPAC

AF:

0.376

AC:

1451

ESP6500AA

AF:

0.186

AC:

818

ESP6500EA

AF:

0.390

AC:

3352

ExAC

AF:

0.407

AC:

49364

Asia WGS

AF:

0.528

AC:

1836

AN:

3478

EpiCase

AF:

0.388

EpiControl

AF:

0.385

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.074

BayesDel_addAF

Benign

-0.69

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Benign

0.83

DEOGEN2

Benign

0.033

Eigen

Uncertain

0.21

Eigen_PC

Benign

-0.081

FATHMM_MKL

Benign

0.033

LIST_S2

Benign

0.29

MetaRNN

Benign

0.0000051

MetaSVM

Benign

-1.0

PROVEAN

Benign

-0.20

REVEL

Benign

0.044

Sift

Benign

0.53

Sift4G

Pathogenic

0.0

Vest4

0.017

ClinPred

0.0035

GERP RS

1.7

Varity_R

0.031

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.37

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.37

Position offset: 2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over