rs693955

Variant names:

• chr6-44224183-A-C
• rs693955
• NM_001372327.1:c.-52+542A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-44224183-A-C
• chr6-44224183-A-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.-52+542A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 152,060 control chromosomes in the GnomAD database, including 55,202 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 0.85 (55202 hom., cov: 30)
• Consequence: SLC29A1 NM_001372327.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 20 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC29A1	NM_001372327.1	c.-52+542A>C		intron_variant	Intron 1 of 12	ENST00000371755.9	NP_001359256.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC29A1	ENST00000371755.9	c.-52+542A>C		intron_variant	Intron 1 of 12	1	NM_001372327.1	ENSP00000360820.3

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128879 AN: 151942 Hom.: 55143 Cov.: 30

Gnomad AFR AF: 0.963

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.848 AC: 128995 AN: 152060 Hom.: 55202 Cov.: 30 AF XY: 0.847 AC XY: 62949 AN XY: 74334

African (AFR) AF: 0.963 AC: 39939 AN: 41478

American (AMR) AF: 0.757 AC: 11561 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3004 AN: 3470

East Asian (EAS) AF: 0.713 AC: 3674 AN: 5156

South Asian (SAS) AF: 0.783 AC: 3766 AN: 4808

European-Finnish (FIN) AF: 0.877 AC: 9288 AN: 10596

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55084 AN: 67970

Other (OTH) AF: 0.857 AC: 1803 AN: 2104

Alfa AF: 0.822 Hom.: 119060

Bravo AF: 0.847

Asia WGS AF: 0.766 AC: 2661 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.9
DANN	Benign	0.62
PhyloP100		-0.23
PromoterAI		-0.038	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs693955; hg19: chr6-44191920;