1-67008820-C-T

Position:

• chr1-67008820-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_015139.3(SLC35D1):​c.959+265G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,832 control chromosomes in the GnomAD database, including 27,736 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.58 (27736 hom., cov: 31)
• Consequence: SLC35D1 NM_015139.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.488

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 1-67008820-C-T is Benign according to our data. Variant chr1-67008820-C-T is described in ClinVar as [Benign]. Clinvar id is 1265910.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC35D1	NM_015139.3	c.959+265G>A		intron_variant		ENST00000235345.6	NP_055954.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC35D1	ENST00000235345.6	c.959+265G>A		intron_variant		1	NM_015139.3	ENSP00000235345	P1

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88070 AN: 151714 Hom.: 27720 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.580 AC: 88108 AN: 151832 Hom.: 27736 Cov.: 31 AF XY: 0.585 AC XY: 43395 AN XY: 74214

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.609

Alfa AF: 0.615 Hom.: 3605

Bravo AF: 0.578

Asia WGS AF: 0.757 AC: 2633 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 27, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.74

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: rs2755270; hg19: chr1-67474503;