rs1128930

Variant names:

• chr6-44232588-A-C
• rs1128930
• NM_001372327.1:c.1059+160A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-44232588-A-C
• chr6-44232588-A-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.1059+160A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 644,174 control chromosomes in the GnomAD database, including 35,685 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 0.32 (7986 hom., cov: 33)
  • Exomes 𝑓: 0.33 (27699 hom.)
• Consequence: SLC29A1 NM_001372327.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 9 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC29A1	NM_001372327.1	c.1059+160A>C		intron_variant	Intron 11 of 12	ENST00000371755.9	NP_001359256.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC29A1	ENST00000371755.9	c.1059+160A>C		intron_variant	Intron 11 of 12	1	NM_001372327.1	ENSP00000360820.3

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48405 AN: 152066 Hom.: 7979 Cov.: 33

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.357

GnomAD4 exome AF: 0.328 AC: 161588 AN: 491990 Hom.: 27699 Cov.: 5 AF XY: 0.323 AC XY: 84679 AN XY: 262096

African (AFR) AF: 0.260 AC: 3397 AN: 13060

American (AMR) AF: 0.308 AC: 5992 AN: 19424

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 5138 AN: 14318

East Asian (EAS) AF: 0.237 AC: 7557 AN: 31868

South Asian (SAS) AF: 0.201 AC: 9752 AN: 48570

European-Finnish (FIN) AF: 0.406 AC: 13527 AN: 33354

Middle Eastern (MID) AF: 0.386 AC: 810 AN: 2100

European-Non Finnish (NFE) AF: 0.352 AC: 106151 AN: 301754

Other (OTH) AF: 0.336 AC: 9264 AN: 27542

GnomAD4 genome AF: 0.318 AC: 48438 AN: 152184 Hom.: 7986 Cov.: 33 AF XY: 0.319 AC XY: 23725 AN XY: 74388

African (AFR) AF: 0.247 AC: 10260 AN: 41518

American (AMR) AF: 0.333 AC: 5091 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1238 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1492 AN: 5186

South Asian (SAS) AF: 0.200 AC: 965 AN: 4826

European-Finnish (FIN) AF: 0.413 AC: 4376 AN: 10586

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23941 AN: 67992

Other (OTH) AF: 0.356 AC: 751 AN: 2112

Alfa AF: 0.343 Hom.: 1097

Bravo AF: 0.310

Asia WGS AF: 0.253 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.036
DANN	Benign	0.62
PhyloP100		-1.3
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: rs1128930; hg19: chr6-44200325; COSMIC: COSV57581098; COSMIC: COSV57581098;