1-67029600-A-G

Position:

• chr1-67029600-A-G

Variant summary

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

The NM_015139.3(SLC35D1):​c.730-7998T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 152,130 control chromosomes in the GnomAD database, including 46,445 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 0.78 (46445 hom., cov: 31)
• Consequence: SLC35D1 NM_015139.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523

Genes affected

SLC35D1 (HGNC:20800): (solute carrier family 35 member D1) Glycosylation of cellular glycoconjugates occurs in the endoplasmic reticulum (ER) and Golgi compartment, and requires transport of nucleotide sugars from the cytosol into the lumen of the ER and Golgi by specific transporters. The protein encoded by this gene resides in the ER, and transports both UDP-glucuronic acid (UDP-GlcA) and UDP-N-acetylgalactosamine (UDP-GalNAc) from the cytoplasm to the ER lumen. It may participate in glucuronidation and/or chondroitin sulfate biosynthesis. Mutations in this gene are associated with Schneckenbecken dysplasia.[provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC35D1	NM_015139.3	c.730-7998T>C		intron_variant		ENST00000235345.6	NP_055954.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC35D1	ENST00000235345.6	c.730-7998T>C		intron_variant		1	NM_015139.3	ENSP00000235345.5

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118372 AN: 152012 Hom.: 46405 Cov.: 31

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.779 AC: 118468 AN: 152130 Hom.: 46445 Cov.: 31 AF XY: 0.779 AC XY: 57880 AN XY: 74318

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.786

Alfa AF: 0.762 Hom.: 18984

Bravo AF: 0.792

Asia WGS AF: 0.873 AC: 3037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.18
DANN	Benign	0.75

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: rs2755250; hg19: chr1-67495283;