dbSNP rs2279861: SLC29A2:c.1059+71T>C (chr11-66365865-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001532.3(SLC29A2):c.1059+71T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 1,407,850 control chromosomes in the GnomAD database, including 329,686 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 0.58 ( 28502 hom., cov: 33)

Exomes 𝑓: 0.69 ( 301184 hom. )

Consequence

SLC29A2
NM_001532.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.439

Publications

20 publications found

Variant links:

Genes affected

SLC29A2 (HGNC:11004): (solute carrier family 29 member 2) The uptake of nucleosides by transporters, such as SLC29A2, is essential for nucleotide synthesis by salvage pathways in cells that lack de novo biosynthetic pathways. Nucleoside transport also plays a key role in the regulation of many physiologic processes through its effect on adenosine concentration at the cell surface (Griffiths et al., 1997 [PubMed 9396714]).[supplied by OMIM, Nov 2008]

SLC29A2 links:

Genome browser will be placed here

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=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001532.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC29A2	NM_001532.3	MANE Select	c.1059+71T>C	intron	N/A	NP_001523.2
SLC29A2	NM_001300868.2		c.1059+71T>C	intron	N/A	NP_001287797.1	Q14542-1
SLC29A2	NM_001300869.2		c.925+71T>C	intron	N/A	NP_001287798.1	Q14542-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC29A2	ENST00000357440.7	TSL:1 MANE Select	c.1059+71T>C	intron	N/A	ENSP00000350024.2	Q14542-1
SLC29A2	ENST00000311161.11	TSL:1	c.925+71T>C	intron	N/A	ENSP00000311250.7	Q14542-4
SLC29A2	ENST00000540386.5	TSL:1	n.*113+71T>C	intron	N/A	ENSP00000444870.1	Q14542-3

Frequencies

GnomAD3 genomes

AF:

0.583

AC:

88612

AN:

151994

Hom.:

28491

Cov.:

show subpopulations

Gnomad AFR

AF:

0.294

Gnomad AMI

AF:

0.820

Gnomad AMR

AF:

0.701

Gnomad ASJ

AF:

0.654

Gnomad EAS

AF:

0.576

Gnomad SAS

AF:

0.809

Gnomad FIN

AF:

0.721

Gnomad MID

AF:

0.589

Gnomad NFE

AF:

0.688

Gnomad OTH

AF:

0.590

GnomAD4 exome

AF:

0.687

AC:

863089

AN:

1255738

Hom.:

301184

AF XY:

0.691

AC XY:

438811

AN XY:

635218

show subpopulations

African (AFR)

AF:

0.277

AC:

8114

AN:

29276

American (AMR)

AF:

0.786

AC:

34823

AN:

44332

Ashkenazi Jewish (ASJ)

AF:

0.656

AC:

16300

AN:

24846

East Asian (EAS)

AF:

0.600

AC:

23194

AN:

38642

South Asian (SAS)

AF:

0.807

AC:

65854

AN:

81586

European-Finnish (FIN)

AF:

0.716

AC:

37933

AN:

53006

Middle Eastern (MID)

AF:

0.621

AC:

3347

AN:

5390

European-Non Finnish (NFE)

AF:

0.689

AC:

637742

AN:

925120

Other (OTH)

AF:

0.668

AC:

35782

AN:

53540

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

14649

29297

43946

58594

73243

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15028

30056

45084

60112

75140

<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:

0.583

AC:

88642

AN:

152112

Hom.:

28502

Cov.:

AF XY:

0.589

AC XY:

43764

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.294

AC:

12177

AN:

41478

American (AMR)

AF:

0.701

AC:

10716

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.654

AC:

2269

AN:

3472

East Asian (EAS)

AF:

0.576

AC:

2978

AN:

5170

South Asian (SAS)

AF:

0.809

AC:

3909

AN:

4832

European-Finnish (FIN)

AF:

0.721

AC:

7625

AN:

10578

Middle Eastern (MID)

AF:

0.595

AC:

175

AN:

294

European-Non Finnish (NFE)

AF:

0.688

AC:

46800

AN:

67988

Other (OTH)

AF:

0.590

AC:

1245

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1676

3352

5029

6705

8381

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

734

1468

2202

2936

3670

<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:

0.660

Hom.:

59192

Bravo

AF:

0.565

Asia WGS

AF:

0.669

AC:

2326

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.96

(source)

DANN

Benign

0.65

PhyloP100

-0.44

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over