rs9394992

Variant names:

• chr6-44228255-C-T
• rs9394992
• NM_001372327.1:c.29+913C>T

Variant summary

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

The NM_001372327.1(SLC29A1):​c.29+913C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,130 control chromosomes in the GnomAD database, including 6,595 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 0.30 (6595 hom., cov: 32)
• Consequence: SLC29A1 NM_001372327.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 13 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC29A1	NM_001372327.1	c.29+913C>T		intron_variant	Intron 2 of 12	ENST00000371755.9	NP_001359256.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC29A1	ENST00000371755.9	c.29+913C>T		intron_variant	Intron 2 of 12	1	NM_001372327.1	ENSP00000360820.3

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44924 AN: 152012 Hom.: 6580 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.296

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.296 AC: 44984 AN: 152130 Hom.: 6595 Cov.: 32 AF XY: 0.296 AC XY: 22020 AN XY: 74364

African (AFR) AF: 0.317 AC: 13143 AN: 41482

American (AMR) AF: 0.259 AC: 3966 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1274 AN: 3472

East Asian (EAS) AF: 0.332 AC: 1720 AN: 5182

South Asian (SAS) AF: 0.247 AC: 1192 AN: 4826

European-Finnish (FIN) AF: 0.312 AC: 3296 AN: 10578

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19389 AN: 67984

Other (OTH) AF: 0.298 AC: 628 AN: 2110

Alfa AF: 0.288 Hom.: 17676

Bravo AF: 0.293

Asia WGS AF: 0.318 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.53
PhyloP100		-1.4
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: rs9394992; hg19: chr6-44195992;