6-44233216-A-G

Position:

• chr6-44233216-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

POLR1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC29A1	NM_001372327.1	c.1260-201A>G		intron_variant		ENST00000371755.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC29A1	ENST00000371755.9	c.1260-201A>G		intron_variant		1	NM_001372327.1	P1

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

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.387

Alfa AF: 0.381 Hom.: 21019

Bravo AF: 0.348

Asia WGS AF: 0.257 AC: 893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.53
DANN	Benign	0.55

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

Publications

LitVar

Other links and lift over

dbSNP: rs760370; hg19: chr6-44200953;