6-44233216-A-G

Variant names:

• chr6-44233216-A-G
• rs760370
• NM_001372327.1:c.1260-201A>G

Variant summary

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

The NM_001372327.1(SLC29A1):​c.1260-201A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,918 control chromosomes in the GnomAD database, including 9,836 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 0.36 (9836 hom., cov: 32)
• Consequence: SLC29A1 NM_001372327.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 37 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 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.1260-201A>G		intron	N/A	NP_001359256.1
	SLC29A1	NM_001304462.2		c.1497-201A>G		intron	N/A	NP_001291391.1
	SLC29A1	NM_001304465.2		c.1338-201A>G		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.1260-201A>G		intron	N/A	ENSP00000360820.3
	SLC29A1	ENST00000371708.1	TSL:1	c.1260-201A>G		intron	N/A	ENSP00000360773.1
	SLC29A1	ENST00000393844.7	TSL:1	c.1260-201A>G		intron	N/A	ENSP00000377427.1

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53892 AN: 151800 Hom.: 9829 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.355 AC: 53931 AN: 151918 Hom.: 9836 Cov.: 32 AF XY: 0.354 AC XY: 26264 AN XY: 74242

African (AFR) AF: 0.288 AC: 11924 AN: 41420

American (AMR) AF: 0.348 AC: 5316 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1310 AN: 3472

East Asian (EAS) AF: 0.285 AC: 1471 AN: 5158

South Asian (SAS) AF: 0.209 AC: 1008 AN: 4824

European-Finnish (FIN) AF: 0.441 AC: 4654 AN: 10548

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27018 AN: 67906

Other (OTH) AF: 0.387 AC: 818 AN: 2112

Alfa AF: 0.378 Hom.: 44933

Bravo AF: 0.348

Asia WGS AF: 0.257 AC: 893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.53
DANN	Benign	0.55
PhyloP100		-1.5
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: rs760370; hg19: chr6-44200953; COSMIC: COSV107367588; COSMIC: COSV107367588;