chr11-66365865-A-G

Position:

• chr11-66365865-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439

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]

ACMG classification

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	Protein	UniProt
SLC29A2	NM_001532.3	c.1059+71T>C		intron_variant		ENST00000357440.7	NP_001523.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC29A2	ENST00000357440.7	c.1059+71T>C		intron_variant		1	NM_001532.3	ENSP00000350024	P1

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88612 AN: 151994 Hom.: 28491 Cov.: 33

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

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.: 33 AF XY: 0.589 AC XY: 43764 AN XY: 74342

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

Other links and lift over

dbSNP: rs2279861; hg19: chr11-66133336; COSMIC: COSV60804164; COSMIC: COSV60804164;