rs6479272

Variant names:

• chr9-96335245-T-C
• rs6479272
• NM_007001.3:c.752+1472A>G

Variant summary

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

The NM_007001.3(SLC35D2):​c.752+1472A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,160 control chromosomes in the GnomAD database, including 36,360 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 0.68 (36360 hom., cov: 32)
• Consequence: SLC35D2 NM_007001.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835
• Publications: 11 publications found

Genes affected

SLC35D2 (HGNC:20799): (solute carrier family 35 member D2) Nucleotide sugars, which are synthesized in the cytosol or the nucleus, are high-energy donor substrates for glycosyltransferases located in the lumen of the endoplasmic reticulum and Golgi apparatus. Translocation of nucleotide sugars from the cytosol into the lumen compartment is mediated by specific nucleotide sugar transporters, such as SLC35D2 (Suda et al., 2004 [PubMed 15082721]).[supplied by OMIM, Mar 2008]

ENSG00000285269 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007001.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35D2	NM_007001.3	MANE Select	c.752+1472A>G		intron	N/A	NP_008932.2	Q76EJ3-1
	SLC35D2	NM_001286990.2		c.489-11076A>G		intron	N/A	NP_001273919.1	Q76EJ3-2
	SLC35D2	NR_104627.2		n.829+1472A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35D2	ENST00000253270.13	TSL:1 MANE Select	c.752+1472A>G		intron	N/A	ENSP00000253270.7	Q76EJ3-1
	SLC35D2	ENST00000375259.9	TSL:1	c.489-11076A>G		intron	N/A	ENSP00000364408.4	Q76EJ3-2
	ENSG00000285269	ENST00000643789.1		n.353+1472A>G		intron	N/A	ENSP00000494818.1	A0A2R8Y5X9

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103265 AN: 152042 Hom.: 36303 Cov.: 32

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.679 AC: 103380 AN: 152160 Hom.: 36360 Cov.: 32 AF XY: 0.678 AC XY: 50394 AN XY: 74378

African (AFR) AF: 0.866 AC: 35984 AN: 41538

American (AMR) AF: 0.637 AC: 9725 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2223 AN: 3470

East Asian (EAS) AF: 0.870 AC: 4507 AN: 5178

South Asian (SAS) AF: 0.552 AC: 2657 AN: 4814

European-Finnish (FIN) AF: 0.614 AC: 6505 AN: 10592

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39803 AN: 67972

Other (OTH) AF: 0.658 AC: 1391 AN: 2114

Alfa AF: 0.638 Hom.: 48563

Bravo AF: 0.690

Asia WGS AF: 0.717 AC: 2497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.10
DANN	Benign	0.20
PhyloP100		-0.83
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: rs6479272; hg19: chr9-99097527;