6-44226608-G-C

Position:

• chr6-44226608-G-C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332

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]

POLR1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SLC29A1	NM_001372327.1	c.-51-655G>C		intron_variant		ENST00000371755.9	NP_001359256.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC29A1	ENST00000371755.9	c.-51-655G>C		intron_variant		1	NM_001372327.1	ENSP00000360820	P1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23615 AN: 152022 Hom.: 2311 Cov.: 32

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.: 5 AF XY: 0.211 AC XY: 16682 AN XY: 79232

Gnomad4 AFR exome AF: 0.0266

Gnomad4 AMR exome AF: 0.141

Gnomad4 ASJ exome AF: 0.158

Gnomad4 EAS exome AF: 0.258

Gnomad4 SAS exome AF: 0.109

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.217

Gnomad4 OTH exome AF: 0.198

GnomAD4 genome AF: 0.155 AC: 23620 AN: 152140 Hom.: 2309 Cov.: 32 AF XY: 0.154 AC XY: 11489 AN XY: 74368

Gnomad4 AFR AF: 0.0395

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.0944

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.164

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
DANN	Benign	0.74

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

LitVar

Other links and lift over

dbSNP: rs747199; hg19: chr6-44194345;