Variant rs2279861 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC29A2	NM_001532.3 linkuse as main transcript	c.1059+71T>C		intron_variant		ENST00000357440.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC29A2	ENST00000357440.7 linkuse as main transcript	c.1059+71T>C		intron_variant		1	NM_001532.3	P1	Q14542-1

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

Gnomad4 AFR exome

AF:

0.277

Gnomad4 AMR exome

AF:

0.786

Gnomad4 ASJ exome

AF:

0.656

Gnomad4 EAS exome

AF:

0.600

Gnomad4 SAS exome

AF:

0.807

Gnomad4 FIN exome

AF:

0.716

Gnomad4 NFE exome

AF:

0.689

Gnomad4 OTH exome

AF:

0.668

GnomAD4 genome

AF:

0.583

AC:

88642

AN:

152112

Hom.:

28502

Cov.:

AF XY:

0.589

AC XY:

43764

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.294

Gnomad4 AMR

AF:

0.701

Gnomad4 ASJ

AF:

0.654

Gnomad4 EAS

AF:

0.576

Gnomad4 SAS

AF:

0.809

Gnomad4 FIN

AF:

0.721

Gnomad4 NFE

AF:

0.688

Gnomad4 OTH

AF:

0.590

Alfa

AF:

0.668

Hom.:

45781

Bravo

AF:

0.565

Asia WGS

AF:

0.669

AC:

2326

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.96

DANN

Benign

0.65

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

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