NM_001372327.1:c.-51-655G>C

Variant names:

• chr6-44226608-G-C
• rs747199
• NM_001372327.1:c.-51-655G>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.-51-655G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 317,978 control chromosomes in the GnomAD database, including 6,118 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 0.16 (2309 hom., cov: 32)
  • Exomes 𝑓: 0.21 (3809 hom.)
• Consequence: SLC29A1 NM_001372327.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332
• Publications: 24 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 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.-51-655G>C		intron	N/A	NP_001359256.1
	SLC29A1	NM_001304462.2		c.187-655G>C		intron	N/A	NP_001291391.1
	SLC29A1	NM_001304465.2		c.25-652G>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.-51-655G>C		intron	N/A	ENSP00000360820.3
	SLC29A1	ENST00000393844.7	TSL:1	c.-51-655G>C		intron	N/A	ENSP00000377427.1
	SLC29A1	ENST00000371740.10	TSL:1	c.-52+441G>C		intron	N/A	ENSP00000360805.6

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23615 AN: 152022 Hom.: 2311 Cov.: 32

Gnomad AFR AF: 0.0397

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.0939

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.162

GnomAD4 exome AF: 0.210 AC: 34866 AN: 165838 Hom.: 3809 Cov.: 5 AF XY: 0.211 AC XY: 16682 AN XY: 79232

African (AFR) AF: 0.0266 AC: 79 AN: 2968

American (AMR) AF: 0.141 AC: 26 AN: 184

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 157 AN: 992

East Asian (EAS) AF: 0.258 AC: 190 AN: 736

South Asian (SAS) AF: 0.109 AC: 343 AN: 3136

European-Finnish (FIN) AF: 0.333 AC: 12 AN: 36

Middle Eastern (MID) AF: 0.189 AC: 63 AN: 334

European-Non Finnish (NFE) AF: 0.217 AC: 32920 AN: 152006

Other (OTH) AF: 0.198 AC: 1076 AN: 5446

GnomAD4 genome AF: 0.155 AC: 23620 AN: 152140 Hom.: 2309 Cov.: 32 AF XY: 0.154 AC XY: 11489 AN XY: 74368

African (AFR) AF: 0.0395 AC: 1642 AN: 41526

American (AMR) AF: 0.153 AC: 2335 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 556 AN: 3468

East Asian (EAS) AF: 0.258 AC: 1332 AN: 5160

South Asian (SAS) AF: 0.0944 AC: 455 AN: 4820

European-Finnish (FIN) AF: 0.248 AC: 2622 AN: 10570

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14033 AN: 67974

Other (OTH) AF: 0.164 AC: 347 AN: 2116

Alfa AF: 0.119 Hom.: 226

Bravo AF: 0.146

Asia WGS AF: 0.188 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.0
DANN	Benign	0.74
PhyloP100		0.33
PromoterAI		0.12	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs747199; hg19: chr6-44194345;