rs3734703

Positions:

• chr6-44233997-C-A

Variant summary

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

The ENST00000371755.9(SLC29A1):​c.*469C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0182 in 163,020 control chromosomes in the GnomAD database, including 255 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 0.018 (240 hom., cov: 32)
  • Exomes 𝑓: 0.016 (15 hom.)
• Consequence: SLC29A1 ENST00000371755.9 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.919

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC29A1	NM_001372327.1	c.*469C>A		3_prime_UTR_variant	13/13	ENST00000371755.9	NP_001359256.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC29A1	ENST00000371755.9	c.*469C>A		3_prime_UTR_variant	13/13	1	NM_001372327.1	ENSP00000360820	P1

Frequencies

GnomAD3 genomes AF: 0.0182 AC: 2777 AN: 152168 Hom.: 238 Cov.: 32

Gnomad AFR AF: 0.00456

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0690

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.0219

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000632

Gnomad OTH AF: 0.0278

GnomAD4 exome AF: 0.0161 AC: 173 AN: 10734 Hom.: 15 Cov.: 0 AF XY: 0.0162 AC XY: 93 AN XY: 5732

Gnomad4 AFR exome AF: 0.00538

Gnomad4 AMR exome AF: 0.0696

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.259

Gnomad4 SAS exome AF: 0.0208

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000910

Gnomad4 OTH exome AF: 0.0260

GnomAD4 genome AF: 0.0183 AC: 2786 AN: 152286 Hom.: 240 Cov.: 32 AF XY: 0.0205 AC XY: 1528 AN XY: 74462

Gnomad4 AFR AF: 0.00455

Gnomad4 AMR AF: 0.0698

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.0219

Gnomad4 FIN AF: 0.000377

Gnomad4 NFE AF: 0.000632

Gnomad4 OTH AF: 0.0294

Alfa AF: 0.00727 Hom.: 148

Bravo AF: 0.0245

Asia WGS AF: 0.149 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.5
DANN	Benign	0.65
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		3.1

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: rs3734703; hg19: chr6-44201734;