ENST00000393844.7:c.-52+1681G>A

Variant names:

• chr6-44221463-G-A
• rs3778504
• ENST00000393844.7:c.-52+1681G>A

Variant summary

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

The ENST00000393844.7(SLC29A1):​c.-52+1681G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0238 in 393,784 control chromosomes in the GnomAD database, including 226 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 0.031 (134 hom., cov: 32)
  • Exomes 𝑓: 0.019 (92 hom.)
• Consequence: SLC29A1 ENST00000393844.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 5 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0728 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000393844.7. 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_001304462.2		c.87-123G>A		intron	N/A	NP_001291391.1
	SLC29A1	NM_001304465.2		c.24+1681G>A		intron	N/A	NP_001291394.1
	SLC29A1	NM_001304466.2		c.24+1681G>A		intron	N/A	NP_001291395.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC29A1	ENST00000393844.7	TSL:1	c.-52+1681G>A		intron	N/A	ENSP00000377427.1
	SLC29A1	ENST00000892039.1		c.-381G>A		5_prime_UTR	Exon 1 of 14	ENSP00000562098.1
	SLC29A1	ENST00000967782.1		c.-52+1681G>A		intron	N/A	ENSP00000637841.1

Frequencies

GnomAD3 genomes AF: 0.0309 AC: 4702 AN: 152174 Hom.: 133 Cov.: 32

Gnomad AFR AF: 0.0749

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0146

Gnomad ASJ AF: 0.00605

Gnomad EAS AF: 0.0496

Gnomad SAS AF: 0.0389

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0311

GnomAD4 exome AF: 0.0194 AC: 4680 AN: 241492 Hom.: 92 AF XY: 0.0209 AC XY: 2799 AN XY: 134180

African (AFR) AF: 0.0800 AC: 534 AN: 6672

American (AMR) AF: 0.00934 AC: 166 AN: 17770

Ashkenazi Jewish (ASJ) AF: 0.00521 AC: 30 AN: 5758

East Asian (EAS) AF: 0.0428 AC: 372 AN: 8696

South Asian (SAS) AF: 0.0364 AC: 1738 AN: 47794

European-Finnish (FIN) AF: 0.0178 AC: 176 AN: 9894

Middle Eastern (MID) AF: 0.0290 AC: 54 AN: 1860

European-Non Finnish (NFE) AF: 0.0106 AC: 1392 AN: 131682

Other (OTH) AF: 0.0192 AC: 218 AN: 11366

GnomAD4 genome AF: 0.0309 AC: 4711 AN: 152292 Hom.: 134 Cov.: 32 AF XY: 0.0316 AC XY: 2355 AN XY: 74464

African (AFR) AF: 0.0750 AC: 3115 AN: 41542

American (AMR) AF: 0.0145 AC: 222 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.00605 AC: 21 AN: 3470

East Asian (EAS) AF: 0.0499 AC: 259 AN: 5188

South Asian (SAS) AF: 0.0387 AC: 187 AN: 4832

European-Finnish (FIN) AF: 0.0137 AC: 146 AN: 10620

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0102 AC: 695 AN: 68016

Other (OTH) AF: 0.0303 AC: 64 AN: 2112

Alfa AF: 0.0199 Hom.: 299

Bravo AF: 0.0321

Asia WGS AF: 0.0460 AC: 160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.65
DANN	Benign	0.54
PhyloP100		-1.2
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: rs3778504; hg19: chr6-44189200;