rs324148

Variant names:

• chr6-44228841-T-C
• rs324148
• NM_001372327.1:c.30-549T>C

Variant summary

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

The NM_001372327.1(SLC29A1):​c.30-549T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,236 control chromosomes in the GnomAD database, including 46,901 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 0.78 (46901 hom., cov: 34)
• Consequence: SLC29A1 NM_001372327.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443
• Publications: 19 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 (AFR) allele frequency at 95% confidence interval = 0.888 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC29A1	NM_001372327.1	MANE Select	c.30-549T>C		intron	N/A	NP_001359256.1
	SLC29A1	NM_001304462.2		c.267-549T>C		intron	N/A	NP_001291391.1
	SLC29A1	NM_001304465.2		c.108-549T>C		intron	N/A	NP_001291394.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC29A1	ENST00000371755.9	TSL:1 MANE Select	c.30-549T>C		intron	N/A	ENSP00000360820.3
	SLC29A1	ENST00000371708.1	TSL:1	c.30-549T>C		intron	N/A	ENSP00000360773.1
	SLC29A1	ENST00000393844.7	TSL:1	c.30-549T>C		intron	N/A	ENSP00000377427.1

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118845 AN: 152118 Hom.: 46846 Cov.: 34

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.781 AC: 118954 AN: 152236 Hom.: 46901 Cov.: 34 AF XY: 0.782 AC XY: 58190 AN XY: 74442

African (AFR) AF: 0.896 AC: 37213 AN: 41550

American (AMR) AF: 0.758 AC: 11588 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2582 AN: 3470

East Asian (EAS) AF: 0.717 AC: 3711 AN: 5176

South Asian (SAS) AF: 0.731 AC: 3527 AN: 4828

European-Finnish (FIN) AF: 0.788 AC: 8361 AN: 10612

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49489 AN: 67988

Other (OTH) AF: 0.795 AC: 1680 AN: 2112

Alfa AF: 0.752 Hom.: 131675

Bravo AF: 0.785

Asia WGS AF: 0.742 AC: 2581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.57
PhyloP100		0.44
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: rs324148; hg19: chr6-44196578;