9-96369762-C-T

Variant names:

• chr9-96369762-C-T
• rs10820447
• NM_007001.3:c.159-1457G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007001.3(SLC35D2):​c.159-1457G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,960 control chromosomes in the GnomAD database, including 6,119 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 0.24 (6119 hom., cov: 31)
• Consequence: SLC35D2 NM_007001.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35D2	NM_007001.3	c.159-1457G>A		intron_variant	Intron 1 of 11	ENST00000253270.13	NP_008932.2
SLC35D2	NM_001286990.2	c.159-1457G>A		intron_variant	Intron 1 of 8		NP_001273919.1
SLC35D2	NR_104627.2	n.236-1457G>A		intron_variant	Intron 1 of 12
SLC35D2-HSD17B3	NR_182427.1	n.236-1457G>A		intron_variant	Intron 1 of 25

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35D2	ENST00000253270.13	c.159-1457G>A		intron_variant	Intron 1 of 11	1	NM_007001.3	ENSP00000253270.7
SLC35D2	ENST00000375259.9	c.159-1457G>A		intron_variant	Intron 1 of 8	1		ENSP00000364408.4
SLC35D2	ENST00000375257.2	c.159-1457G>A		intron_variant	Intron 1 of 5	2		ENSP00000364406.1
SLC35D2	ENST00000482643.2	n.288-1457G>A		intron_variant	Intron 2 of 8	5

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36189 AN: 151842 Hom.: 6088 Cov.: 31

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.0223

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.239 AC: 36269 AN: 151960 Hom.: 6119 Cov.: 31 AF XY: 0.232 AC XY: 17194 AN XY: 74270

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.0222

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.204

Alfa AF: 0.151 Hom.: 1015

Bravo AF: 0.248

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.65
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs10820447; hg19: chr9-99132044;