rs3734703

Variant names:

• chr6-44233997-C-A
• rs3734703
• NM_001372327.1:c.*469C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001372327.1(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 NM_001372327.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.919
• Publications: 8 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001372327.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC29A1	NM_001372327.1	MANE Select	c.*469C>A		3_prime_UTR	Exon 13 of 13	NP_001359256.1	Q99808-1
	SLC29A1	NM_001304462.2		c.*469C>A		3_prime_UTR	Exon 14 of 14	NP_001291391.1	Q99808-2
	SLC29A1	NM_001304465.2		c.*469C>A		3_prime_UTR	Exon 13 of 13	NP_001291394.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC29A1	ENST00000371755.9	TSL:1 MANE Select	c.*469C>A		3_prime_UTR	Exon 13 of 13	ENSP00000360820.3	Q99808-1
	SLC29A1	ENST00000371708.1	TSL:1	c.*469C>A		3_prime_UTR	Exon 12 of 12	ENSP00000360773.1	Q99808-1
	SLC29A1	ENST00000393844.7	TSL:1	c.*469C>A		3_prime_UTR	Exon 13 of 13	ENSP00000377427.1	Q99808-1

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

African (AFR) AF: 0.00538 AC: 1 AN: 186

American (AMR) AF: 0.0696 AC: 54 AN: 776

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 182

East Asian (EAS) AF: 0.259 AC: 72 AN: 278

South Asian (SAS) AF: 0.0208 AC: 24 AN: 1152

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 910

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 44

European-Non Finnish (NFE) AF: 0.000910 AC: 6 AN: 6590

Other (OTH) AF: 0.0260 AC: 16 AN: 616

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

African (AFR) AF: 0.00455 AC: 189 AN: 41554

American (AMR) AF: 0.0698 AC: 1067 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3470

East Asian (EAS) AF: 0.254 AC: 1313 AN: 5174

South Asian (SAS) AF: 0.0219 AC: 106 AN: 4832

European-Finnish (FIN) AF: 0.000377 AC: 4 AN: 10622

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000632 AC: 43 AN: 68022

Other (OTH) AF: 0.0294 AC: 62 AN: 2110

Alfa AF: 0.00804 Hom.: 185

Bravo AF: 0.0245

Asia WGS AF: 0.149 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.5
DANN	Benign	0.65
PhyloP100		-0.92
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		3.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3734703; hg19: chr6-44201734;