Genetic Variant SLC17A2:c.28+10C>T (chr6-25925759-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.737

Publications

38 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC17A2	NM_001286123.3 link	c.28+10C>T		intron_variant	Intron 2 of 11	ENST00000377850.8	NP_001273052.1	O00624-3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC17A2	ENST00000377850.8 link	c.28+10C>T	intron_variant	Intron 2 of 11	5	NM_001286123.3	ENSP00000367081.3	O00624-3
SLC17A2	ENST00000360488.7 link	c.28+10C>T	intron_variant	Intron 2 of 10	1		ENSP00000353677.3	O00624-2
SLC17A2	ENST00000265425.3 link	c.28+10C>T	intron_variant	Intron 1 of 10	5		ENSP00000265425.3	O00624-1

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

16037

AN:

152114

Hom.:

1023

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.0750

AC:

18852

AN:

251480

AF XY:

0.0733

show subpopulations

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 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.:

AF XY:

0.0973

AC XY:

70688

AN XY:

726584

show subpopulations

African (AFR)

AF:

0.176

AC:

5871

AN:

33448

American (AMR)

AF:

0.0501

AC:

2242

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.0381

AC:

997

AN:

26134

East Asian (EAS)

AF:

0.00914

AC:

363

AN:

39698

South Asian (SAS)

AF:

0.0396

AC:

3417

AN:

86238

European-Finnish (FIN)

AF:

0.0476

AC:

2540

AN:

53416

Middle Eastern (MID)

AF:

0.0692

AC:

399

AN:

5768

European-Non Finnish (NFE)

AF:

0.113

AC:

125045

AN:

1110498

Other (OTH)

AF:

0.0909

AC:

5486

AN:

60348

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

5890

11780

17671

23561

29451

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4706

9412

14118

18824

23530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.105

AC:

16044

AN:

152232

Hom.:

1024

Cov.:

AF XY:

0.0996

AC XY:

7412

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.171

AC:

7110

AN:

41498

American (AMR)

AF:

0.0749

AC:

1145

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0372

AC:

129

AN:

3470

East Asian (EAS)

AF:

0.0185

AC:

AN:

5182

South Asian (SAS)

AF:

0.0290

AC:

140

AN:

4830

European-Finnish (FIN)

AF:

0.0474

AC:

503

AN:

10616

Middle Eastern (MID)

AF:

0.0952

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0981

AC:

6675

AN:

68022

Other (OTH)

AF:

0.0989

AC:

209

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

714

1427

2141

2854

3568

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

344

516

688

860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.101

Hom.:

2967

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

(source)

DANN

Benign

0.59

PhyloP100

-0.74

PromoterAI

0.0027

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over