Genetic Variant SLC29A1:c.-51-655G>C (chr6-44226608-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001372327.1(SLC29A1):c.-51-655G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 317,978 control chromosomes in the GnomAD database, including 6,118 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 0.16 ( 2309 hom., cov: 32)

Exomes 𝑓: 0.21 ( 3809 hom. )

Consequence

SLC29A1
NM_001372327.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.332

Publications

24 publications found

Variant links:

Genes affected

SLC29A1 (HGNC:11003): (solute carrier family 29 member 1 (Augustine blood group)) This gene is a member of the equilibrative nucleoside transporter family. The gene encodes a transmembrane glycoprotein that localizes to the plasma and mitochondrial membranes and mediates the cellular uptake of nucleosides from the surrounding medium. The protein is categorized as an equilibrative (as opposed to concentrative) transporter that is sensitive to inhibition by nitrobenzylthioinosine (NBMPR). Nucleoside transporters are required for nucleotide synthesis in cells that lack de novo nucleoside synthesis pathways, and are also necessary for the uptake of cytotoxic nucleosides used for cancer and viral chemotherapies. Multiple alternatively spliced variants, encoding the same protein, have been found for this gene. [provided by RefSeq, Jul 2008]

SLC29A1 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC29A1	NM_001372327.1 link	c.-51-655G>C		intron_variant	Intron 1 of 12	ENST00000371755.9	NP_001359256.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC29A1	ENST00000371755.9 link	c.-51-655G>C		intron_variant	Intron 1 of 12	1	NM_001372327.1	ENSP00000360820.3

Frequencies

GnomAD3 genomes

AF:

0.155

AC:

23615

AN:

152022

Hom.:

2311

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0397

Gnomad AMI

AF:

0.279

Gnomad AMR

AF:

0.152

Gnomad ASJ

AF:

0.160

Gnomad EAS

AF:

0.259

Gnomad SAS

AF:

0.0939

Gnomad FIN

AF:

0.248

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.162

GnomAD4 exome

AF:

0.210

AC:

34866

AN:

165838

Hom.:

3809

Cov.:

AF XY:

0.211

AC XY:

16682

AN XY:

79232

show subpopulations

African (AFR)

AF:

0.0266

AC:

AN:

2968

American (AMR)

AF:

0.141

AC:

AN:

184

Ashkenazi Jewish (ASJ)

AF:

0.158

AC:

157

AN:

992

East Asian (EAS)

AF:

0.258

AC:

190

AN:

736

South Asian (SAS)

AF:

0.109

AC:

343

AN:

3136

European-Finnish (FIN)

AF:

0.333

AC:

AN:

Middle Eastern (MID)

AF:

0.189

AC:

AN:

334

European-Non Finnish (NFE)

AF:

0.217

AC:

32920

AN:

152006

Other (OTH)

AF:

0.198

AC:

1076

AN:

5446

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

1374

2748

4122

5496

6870

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1542

3084

4626

6168

7710

<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:

0.155

AC:

23620

AN:

152140

Hom.:

2309

Cov.:

AF XY:

0.154

AC XY:

11489

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.0395

AC:

1642

AN:

41526

American (AMR)

AF:

0.153

AC:

2335

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.160

AC:

556

AN:

3468

East Asian (EAS)

AF:

0.258

AC:

1332

AN:

5160

South Asian (SAS)

AF:

0.0944

AC:

455

AN:

4820

European-Finnish (FIN)

AF:

0.248

AC:

2622

AN:

10570

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.206

AC:

14033

AN:

67974

Other (OTH)

AF:

0.164

AC:

347

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1001

2002

3002

4003

5004

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.119

Hom.:

226

Bravo

AF:

0.146

Asia WGS

AF:

0.188

AC:

655

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

9.0

(source)

DANN

Benign

0.74

PhyloP100

0.33

PromoterAI

0.12

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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