rs6479272

Positions:

• chr9-96335245-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

SLC35D2-HSD17B3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35D2	NM_007001.3	c.752+1472A>G		intron_variant		ENST00000253270.13
SLC35D2-HSD17B3	NR_182427.1	n.829+1472A>G		intron_variant, non_coding_transcript_variant
SLC35D2	NM_001286990.2	c.489-11076A>G		intron_variant
SLC35D2	NR_104627.2	n.829+1472A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35D2	ENST00000253270.13	c.752+1472A>G		intron_variant		1	NM_007001.3	P1
SLC35D2	ENST00000375259.9	c.489-11076A>G		intron_variant		1
SLC35D2	ENST00000490599.2	c.444+1472A>G		intron_variant		2
SLC35D2	ENST00000650065.1	c.*529+1472A>G		intron_variant, NMD_transcript_variant

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

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.658

Alfa AF: 0.608 Hom.: 28350

Bravo AF: 0.690

Asia WGS AF: 0.717 AC: 2497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.10
DANN	Benign	0.20

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: rs6479272; hg19: chr9-99097527;